diff --git a/fhircraft/fhir/packages/client.py b/fhircraft/fhir/packages/client.py
index 5577c1ed..062fa091 100644
--- a/fhircraft/fhir/packages/client.py
+++ b/fhircraft/fhir/packages/client.py
@@ -263,8 +263,8 @@ def _process_package_tar(
         Args:
             tar_file: Opened tar file containing the package
         """
-        results_count = 0
         errors = []
+        results = []
 
         # First, look for package.json to find dependencies
         if install_dependencies:
@@ -287,12 +287,13 @@ def _process_package_tar(
                             if f"{dependency}@{version}" in self.history:
                                 continue
                             try:
-                                self.load_resources_from_package(
+                                dependency_results = self.load_resources_from_package(
                                     target_resource,
                                     dependency,
                                     version,
                                     fail_if_exists=False,
                                 )
+                                results.extend(dependency_results)
                             except Exception as e:
                                 errors.append(
                                     f"Failed to download and load dependency {dependency}: {e}"
@@ -301,7 +302,6 @@ def _process_package_tar(
                     errors.append(
                         f"Error processing package.json looking for dependencies: {e}"
                     )
-        results = []
         for member in tar_file.getmembers():
             if not member.isfile():
                 continue
@@ -324,7 +324,6 @@ def _process_package_tar(
                         # Check if it's a StructureDefinition resource
                         if json_data.get("resourceType") == target_resource:
                             results.append(json_data)
-                            results_count += 1
 
                 except Exception as e:
                     errors.append(f"Error processing {member.name}: {e}")
diff --git a/fhircraft/fhir/resources/definitions/registry.py b/fhircraft/fhir/resources/definitions/registry.py
index de0ff9fe..3bd3c8e2 100644
--- a/fhircraft/fhir/resources/definitions/registry.py
+++ b/fhircraft/fhir/resources/definitions/registry.py
@@ -9,6 +9,7 @@
 from dataclasses import asdict, dataclass, field
 from pathlib import Path
 from typing import Any, Dict, List, Optional, Tuple, Union
+import warnings
 
 import requests
 from pydantic import BaseModel
@@ -293,13 +294,30 @@ def download_url(url: str) -> Dict[str, Any]:
         response.raise_for_status()
         return response.json()
 
-    def download_package(self, package_name: str, version: str) -> None:
+    def download_package(
+        self,
+        package_name: str,
+        version: str,
+        skip_invalid: bool = False,
+        include_dependencies: bool = True,
+    ) -> None:
         """Download a package from the registry and add its structure definitions to the registry."""
         for sd in self._package_client.load_resources_from_package(
-            "StructureDefinition", package_name, version
+            "StructureDefinition",
+            package_name,
+            version,
+            install_dependencies=include_dependencies,
         ):
-            structure_definition = self._validate_structure_definition(sd)
-            self.add(structure_definition)
+            try:
+                structure_definition = self._validate_structure_definition(sd)
+                self.add(structure_definition)
+            except ValueError as e:
+                if not skip_invalid:
+                    raise e
+                else:
+                    warnings.warn(
+                        f"Skipping invalid structure definition {sd.get('url', 'unknown')} in package {package_name} version {version}:\n{e}"
+                    )
 
     def set_registry_base_url(self, base_url: str) -> None:
         """Change the package registry base URL."""
diff --git a/fhircraft/fhir/resources/factory/core.py b/fhircraft/fhir/resources/factory/core.py
index 0320de4c..2bafb27e 100644
--- a/fhircraft/fhir/resources/factory/core.py
+++ b/fhircraft/fhir/resources/factory/core.py
@@ -108,15 +108,25 @@ def build(
 
         return self._build(structure_definition, mixins=mixins, mode=mode)
 
-    def register_package(self, package_name: str, version: str) -> None:
+    def register_package(
+        self,
+        package_name: str,
+        version: str,
+        skip_invalid: bool = False,
+        include_dependencies: bool = True,
+    ) -> None:
         """
         Download and register all StructureDefinitions from a FHIR npm package.
 
         Args:
             package_name: Package identifier (e.g. ``"hl7.fhir.us.mcode"``).
             version: Package version string (e.g. ``"1.0.0"``).
+            skip_invalid: Whether to skip invalid StructureDefinitions.
+            include_dependencies: Whether to include dependencies when downloading the package.
         """
-        self.definition_registry.download_package(package_name, version)
+        self.definition_registry.download_package(
+            package_name, version, skip_invalid, include_dependencies
+        )
 
     def register(
         self,
diff --git a/test/test_fhir_packages_client.py b/test/test_fhir_packages_client.py
index fbb45f6f..c94f3152 100644
--- a/test/test_fhir_packages_client.py
+++ b/test/test_fhir_packages_client.py
@@ -1,6 +1,8 @@
 """Tests for FHIR Package Registry client."""
 
+import io
 import json
+import tarfile
 from unittest.mock import Mock, patch
 
 import pytest
@@ -13,6 +15,29 @@
 )
 
 
+# ---------------------------------------------------------------------------
+# Helpers
+# ---------------------------------------------------------------------------
+
+
+def _make_tar(files: dict) -> tarfile.TarFile:
+    """Build an in-memory TarFile from a dict of {filename: bytes_or_str}."""
+    buf = io.BytesIO()
+    with tarfile.open(fileobj=buf, mode="w:gz") as tf:
+        for name, content in files.items():
+            if isinstance(content, str):
+                content = content.encode("utf-8")
+            info = tarfile.TarInfo(name=name)
+            info.size = len(content)
+            tf.addfile(info, io.BytesIO(content))
+    buf.seek(0)
+    return tarfile.open(fileobj=buf, mode="r:gz")
+
+
+def _sd(url: str, resource_type: str = "StructureDefinition") -> str:
+    return json.dumps({"resourceType": resource_type, "url": url})
+
+
 class TestFHIRPackageRegistryClient:
     """Test cases for FHIRPackageRegistryClient."""
 
@@ -194,3 +219,250 @@ def test_package_metadata_minimal(self):
         assert metadata.dist_tags is None
         assert metadata.versions is None
         assert metadata.versions is None
+
+
+# ===========================================================================
+# TestProcessPackageTar
+# ===========================================================================
+
+
+class TestProcessPackageTar:
+    """Tests for FHIRPackageRegistryClient._process_package_tar."""
+
+    def test_returns_sds_from_package(self):
+        """SDs in the tar file are extracted and returned."""
+        sd_url = "http://example.org/StructureDefinition/MyProfile"
+        tar = _make_tar(
+            {
+                "package/StructureDefinition-MyProfile.json": _sd(sd_url),
+            }
+        )
+        client = FHIRPackageRegistryClient()
+        results, errors = client._process_package_tar("StructureDefinition", tar)
+        assert errors == []
+        assert len(results) == 1
+        assert results[0]["url"] == sd_url
+
+    def test_no_dependencies_when_package_json_absent(self):
+        """When there is no package.json the dependency loop is skipped."""
+        sd_url = "http://example.org/StructureDefinition/MyProfile"
+        tar = _make_tar(
+            {
+                "package/StructureDefinition-MyProfile.json": _sd(sd_url),
+            }
+        )
+        client = FHIRPackageRegistryClient()
+        with patch.object(client, "load_resources_from_package") as mock_load:
+            results, errors = client._process_package_tar("StructureDefinition", tar)
+        mock_load.assert_not_called()
+        assert len(results) == 1
+
+    def test_dependency_sds_included_in_results(self):
+        """SDs from dependencies are merged into the result list."""
+        dep_url = "http://example.org/StructureDefinition/DepProfile"
+        dep_sd = {"resourceType": "StructureDefinition", "url": dep_url}
+
+        package_json = json.dumps(
+            {"name": "my.pkg", "version": "1.0.0", "dependencies": {"dep.pkg": "1.0.0"}}
+        )
+        tar = _make_tar({"package/package.json": package_json})
+
+        client = FHIRPackageRegistryClient()
+        with patch.object(
+            client,
+            "load_resources_from_package",
+            return_value=[dep_sd],
+        ) as mock_load:
+            results, errors = client._process_package_tar("StructureDefinition", tar)
+
+        mock_load.assert_called_once_with(
+            "StructureDefinition", "dep.pkg", "1.0.0", fail_if_exists=False
+        )
+        assert errors == []
+        assert dep_sd in results
+
+    def test_multiple_dependency_sds_all_included(self):
+        """SDs from multiple dependencies are all present in results."""
+        dep_a = {"resourceType": "StructureDefinition", "url": "http://example.org/A"}
+        dep_b = {"resourceType": "StructureDefinition", "url": "http://example.org/B"}
+
+        package_json = json.dumps(
+            {
+                "name": "my.pkg",
+                "version": "1.0.0",
+                "dependencies": {"dep.a": "1.0.0", "dep.b": "2.0.0"},
+            }
+        )
+        tar = _make_tar({"package/package.json": package_json})
+
+        client = FHIRPackageRegistryClient()
+        with patch.object(
+            client,
+            "load_resources_from_package",
+            side_effect=[[dep_a], [dep_b]],
+        ):
+            results, errors = client._process_package_tar("StructureDefinition", tar)
+
+        assert errors == []
+        assert dep_a in results
+        assert dep_b in results
+
+    def test_already_loaded_dependency_is_skipped(self):
+        """A dependency already in history is not re-downloaded."""
+        package_json = json.dumps(
+            {"name": "my.pkg", "version": "1.0.0", "dependencies": {"dep.pkg": "1.0.0"}}
+        )
+        tar = _make_tar({"package/package.json": package_json})
+
+        client = FHIRPackageRegistryClient()
+        client.history.add("dep.pkg@1.0.0")  # mark as already loaded
+
+        with patch.object(client, "load_resources_from_package") as mock_load:
+            results, errors = client._process_package_tar("StructureDefinition", tar)
+
+        mock_load.assert_not_called()
+        assert errors == []
+
+    def test_dependency_failure_recorded_as_error_not_raised(self):
+        """A failing dependency download is recorded in errors, not raised."""
+        package_json = json.dumps(
+            {"name": "my.pkg", "version": "1.0.0", "dependencies": {"bad.dep": "9.9.9"}}
+        )
+        tar = _make_tar({"package/package.json": package_json})
+
+        client = FHIRPackageRegistryClient()
+        with patch.object(
+            client,
+            "load_resources_from_package",
+            side_effect=PackageNotFoundError("not found"),
+        ):
+            results, errors = client._process_package_tar("StructureDefinition", tar)
+
+        assert len(errors) == 1
+        assert "bad.dep" in errors[0]
+        assert results == []
+
+    def test_install_dependencies_false_skips_dependency_processing(self):
+        """When install_dependencies=False the dependency block is never entered."""
+        package_json = json.dumps(
+            {"name": "my.pkg", "version": "1.0.0", "dependencies": {"dep.pkg": "1.0.0"}}
+        )
+        tar = _make_tar({"package/package.json": package_json})
+
+        client = FHIRPackageRegistryClient()
+        with patch.object(client, "load_resources_from_package") as mock_load:
+            results, errors = client._process_package_tar(
+                "StructureDefinition", tar, install_dependencies=False
+            )
+
+        mock_load.assert_not_called()
+
+
+# ===========================================================================
+# TestLoadResourcesFromPackage – dependency propagation (regression)
+# ===========================================================================
+
+
+class TestLoadResourcesFromPackageDependencies:
+    """Regression tests for the bug where dependency SDs were not returned."""
+
+    def _make_download_mock(self, pkg_sd_url: str, dep_sd_url: str):
+        """
+        Return a side_effect callable that serves two packages:
+          - "my.pkg/1.0.0"  → tar with package.json declaring dep.pkg + one SD
+          - "dep.pkg/1.0.0" → tar with one SD
+        """
+        pkg_sd = _sd(pkg_sd_url)
+        dep_sd = _sd(dep_sd_url)
+        pkg_package_json = json.dumps(
+            {"name": "my.pkg", "version": "1.0.0", "dependencies": {"dep.pkg": "1.0.0"}}
+        )
+        dep_package_json = json.dumps(
+            {"name": "dep.pkg", "version": "1.0.0", "dependencies": {}}
+        )
+
+        pkg_tar = _make_tar(
+            {
+                "package/package.json": pkg_package_json,
+                "package/StructureDefinition-PkgProfile.json": pkg_sd,
+            }
+        )
+        dep_tar = _make_tar(
+            {
+                "package/package.json": dep_package_json,
+                "package/StructureDefinition-DepProfile.json": dep_sd,
+            }
+        )
+
+        tars = {"my.pkg": pkg_tar, "dep.pkg": dep_tar}
+
+        def _download(name, version, extract=False):
+            tf = tars[name]
+            assert tf.fileobj is not None, "TarFile must have fileobj for mock to work"
+            # Re-open the same buffer for each download call
+            tf.fileobj.seek(0)
+            return tarfile.open(fileobj=tf.fileobj, mode="r:gz")
+
+        return _download
+
+    @patch("requests.Session.get")
+    def test_register_package_also_returns_dependency_sds(self, mock_get):
+        """
+        Regression test: load_resources_from_package must include SDs from
+        transitive dependencies in its return value, not only the top-level package.
+        """
+        pkg_sd_url = "http://example.org/StructureDefinition/PkgProfile"
+        dep_sd_url = "http://example.org/StructureDefinition/DepProfile"
+
+        # Mock the HTTP layer so download_package calls get real tar content
+        def _http_side_effect(url, **kwargs):
+            resp = Mock()
+            resp.status_code = 200
+            if "my.pkg" in url:
+                pkg_package_json = json.dumps(
+                    {
+                        "name": "my.pkg",
+                        "version": "1.0.0",
+                        "dependencies": {"dep.pkg": "1.0.0"},
+                    }
+                )
+                buf = io.BytesIO()
+                with tarfile.open(fileobj=buf, mode="w:gz") as tf:
+                    for name, content in {
+                        "package/package.json": pkg_package_json,
+                        "package/StructureDefinition-PkgProfile.json": _sd(pkg_sd_url),
+                    }.items():
+                        b = content.encode("utf-8")
+                        info = tarfile.TarInfo(name=name)
+                        info.size = len(b)
+                        tf.addfile(info, io.BytesIO(b))
+                resp.content = buf.getvalue()
+            else:
+                dep_package_json = json.dumps(
+                    {"name": "dep.pkg", "version": "1.0.0", "dependencies": {}}
+                )
+                buf = io.BytesIO()
+                with tarfile.open(fileobj=buf, mode="w:gz") as tf:
+                    for name, content in {
+                        "package/package.json": dep_package_json,
+                        "package/StructureDefinition-DepProfile.json": _sd(dep_sd_url),
+                    }.items():
+                        b = content.encode("utf-8")
+                        info = tarfile.TarInfo(name=name)
+                        info.size = len(b)
+                        tf.addfile(info, io.BytesIO(b))
+                resp.content = buf.getvalue()
+            return resp
+
+        mock_get.side_effect = _http_side_effect
+
+        client = FHIRPackageRegistryClient()
+        results = client.load_resources_from_package(
+            "StructureDefinition", "my.pkg", "1.0.0"
+        )
+        urls = [r["url"] for r in results]
+
+        assert pkg_sd_url in urls, "Top-level package SD must be in results"
+        assert (
+            dep_sd_url in urls
+        ), "Dependency SD must also be in results (regression: was silently dropped)"
diff --git a/test/test_fhir_resources_definitions_registry.py b/test/test_fhir_resources_definitions_registry.py
index 3000a9b0..ae539c0f 100644
--- a/test/test_fhir_resources_definitions_registry.py
+++ b/test/test_fhir_resources_definitions_registry.py
@@ -365,10 +365,49 @@ def test_download_package__calls_load_resources_from_package():
         reg.download_package("hl7.fhir.r4b.core", "4.3.0")
 
     reg._package_client.load_resources_from_package.assert_called_once_with(
-        "StructureDefinition", "hl7.fhir.r4b.core", "4.3.0"
+        "StructureDefinition", "hl7.fhir.r4b.core", "4.3.0", install_dependencies=True
     )
 
 
+def test_download_package__include_dependencies_true_passes_flag():
+    reg = make_registry()
+    sd = make_sd()
+    reg._package_client = MagicMock()
+    reg._package_client.load_resources_from_package.return_value = [{"url": SD_URL}]
+
+    with patch.object(reg, "_validate_structure_definition", return_value=sd):
+        reg.download_package("pkg", "1.0", include_dependencies=True)
+
+    _, kwargs = reg._package_client.load_resources_from_package.call_args
+    assert kwargs["install_dependencies"] is True
+
+
+def test_download_package__include_dependencies_false_passes_flag():
+    reg = make_registry()
+    sd = make_sd()
+    reg._package_client = MagicMock()
+    reg._package_client.load_resources_from_package.return_value = [{"url": SD_URL}]
+
+    with patch.object(reg, "_validate_structure_definition", return_value=sd):
+        reg.download_package("pkg", "1.0", include_dependencies=False)
+
+    _, kwargs = reg._package_client.load_resources_from_package.call_args
+    assert kwargs["install_dependencies"] is False
+
+
+def test_download_package__include_dependencies_defaults_to_true():
+    reg = make_registry()
+    sd = make_sd()
+    reg._package_client = MagicMock()
+    reg._package_client.load_resources_from_package.return_value = [{"url": SD_URL}]
+
+    with patch.object(reg, "_validate_structure_definition", return_value=sd):
+        reg.download_package("pkg", "1.0")
+
+    _, kwargs = reg._package_client.load_resources_from_package.call_args
+    assert kwargs["install_dependencies"] is True
+
+
 def test_download_package__adds_each_validated_sd():
     reg = make_registry()
     sd_a = make_sd(url="http://example.org/A")
@@ -386,6 +425,78 @@ def test_download_package__adds_each_validated_sd():
     assert "http://example.org/B" in reg.structure_definitions_by_url
 
 
+def test_download_package__raises_on_invalid_sd_by_default():
+    reg = make_registry()
+    reg._package_client = MagicMock()
+    reg._package_client.load_resources_from_package.return_value = [
+        {"url": "http://example.org/Bad"}
+    ]
+
+    with patch.object(
+        reg,
+        "_validate_structure_definition",
+        side_effect=ValueError("invalid SD"),
+    ):
+        with pytest.raises(ValueError, match="invalid SD"):
+            reg.download_package("pkg", "1.0")
+
+
+def test_download_package__skip_invalid_true_does_not_raise():
+    reg = make_registry()
+    reg._package_client = MagicMock()
+    reg._package_client.load_resources_from_package.return_value = [
+        {"url": "http://example.org/Bad"}
+    ]
+
+    with patch.object(
+        reg,
+        "_validate_structure_definition",
+        side_effect=ValueError("invalid SD"),
+    ):
+        # Should not raise
+        reg.download_package("pkg", "1.0", skip_invalid=True)
+
+
+def test_download_package__skip_invalid_true_emits_warning():
+    reg = make_registry()
+    reg._package_client = MagicMock()
+    reg._package_client.load_resources_from_package.return_value = [
+        {"url": "http://example.org/Bad"}
+    ]
+
+    with patch.object(
+        reg,
+        "_validate_structure_definition",
+        side_effect=ValueError("invalid SD"),
+    ):
+        with pytest.warns(UserWarning, match="http://example.org/Bad"):
+            reg.download_package("pkg", "1.0", skip_invalid=True)
+
+
+def test_download_package__skip_invalid_skips_bad_registers_good():
+    reg = make_registry()
+    sd_good = make_sd(url="http://example.org/Good")
+    reg._package_client = MagicMock()
+    reg._package_client.load_resources_from_package.return_value = [
+        {"url": "http://example.org/Bad"},
+        {"url": "http://example.org/Good"},
+    ]
+
+    with patch.object(
+        reg,
+        "_validate_structure_definition",
+        side_effect=[ValueError("invalid SD"), sd_good],
+    ):
+        import warnings as _warnings
+
+        with _warnings.catch_warnings():
+            _warnings.simplefilter("ignore")
+            reg.download_package("pkg", "1.0", skip_invalid=True)
+
+    assert "http://example.org/Good" in reg.structure_definitions_by_url
+    assert "http://example.org/Bad" not in reg.structure_definitions_by_url
+
+
 # ===========================================================================
 # StructureDefinitionRegistry.from_dict
 # ===========================================================================
diff --git a/test/test_fhir_resources_factory_core.py b/test/test_fhir_resources_factory_core.py
index 2f21ba35..9f80f163 100644
--- a/test/test_fhir_resources_factory_core.py
+++ b/test/test_fhir_resources_factory_core.py
@@ -445,7 +445,9 @@ def test_register_package__delegates_to_registry():
     registry = make_registry()
     factory = FHIRModelFactory(registry=registry, fhir_release="R4")
     factory.register_package("hl7.fhir.us.core", "5.0.1")
-    registry.download_package.assert_called_once_with("hl7.fhir.us.core", "5.0.1")
+    registry.download_package.assert_called_once_with(
+        "hl7.fhir.us.core", "5.0.1", False, True
+    )
 
 
 # ===========================================================================