diff --git a/R/I-methods.r b/R/I-methods.r
index 021c6ad..e9896ca 100644
--- a/R/I-methods.r
+++ b/R/I-methods.r
@@ -161,7 +161,7 @@
   # read the header
   f <- file(filepath, 'r')
   header <- scan(filepath, what='character', sep='\t', comment.char='',
-                 skip=header.index-1, quote='"',
+                 skip=header.index-1, quote='"', strip.white=TRUE,
                  nlines=1, quiet=TRUE)
   # Close the connection
   close(f)
diff --git a/inst/tests/test-input-methods.r b/inst/tests/test-input-methods.r
index 4f97dce..65c166c 100644
--- a/inst/tests/test-input-methods.r
+++ b/inst/tests/test-input-methods.r
@@ -58,6 +58,19 @@ test_that("Whitespace is stripped from fields in mapping file", {
   unlink(map_fp)
 })
 
+test_that("Whitespace is stripped from column names in mapping file", {
+  map_fp <- tempfile()
+  writeLines(c("#SampleID\t A\tB C ", "w\tx\ty"), map_fp)
+  
+  expected_df <- data.frame("x", "y")
+  rownames(expected_df) <- "w"
+  colnames(expected_df) <- c("A", "B C")
+  
+  expect_equal(load.qiime.mapping.file(map_fp), expected_df)
+  
+  unlink(map_fp)
+})
+
 test_that("Comments are ignored in mapping file", {
   map_fp <- tempfile()
   writeLines(c("#SampleID\tA\tB", "# Comment 1", "w\tx\ty", "#C2"), map_fp)