diff --git a/emperor/core.py b/emperor/core.py
index b5684e0d..c981d6d0 100644
--- a/emperor/core.py
+++ b/emperor/core.py
@@ -325,11 +325,22 @@ def _validate_metadata(self, metadata, matrix, ignore_missing_samples,
                              ' to the same dataset.' % kind)
 
         if difference and not ignore_missing_samples:
-            elements = ', '.join(sorted([str(i) for i in difference]))
+            # sort the elements so we have a deterministic output
+            difference = sorted([str(i) for i in difference])
+
+            # if there's more than 5 missing elements, truncate the list
+            if len(difference) > 5:
+                elements = ', '.join(difference[:5])
+                suffix = ("Showing only the first 5 %ss out of %d: %s ..." %
+                          (kind, len(difference), elements))
+            else:
+                elements = ', '.join(difference)
+                suffix = ("Offending %ss: %s" % (kind, elements))
+
             raise KeyError("There are %ss not included in the %s mapping "
                            "file. Override this error by using the "
-                           "`ignore_missing_samples` argument. Offending "
-                           "%ss: %s" % (kind, kind, kind, elements))
+                           "`ignore_missing_samples` argument. %s" %
+                           (kind, kind, suffix))
         elif difference and ignore_missing_samples:
             warnings.warn("%d out of %d %ss have no metadata and are being"
                           " included with a placeholder value." %
diff --git a/tests/test_core.py b/tests/test_core.py
index 6956ce3c..2155445d 100644
--- a/tests/test_core.py
+++ b/tests/test_core.py
@@ -241,6 +241,19 @@ def test_one_dimensional(self):
                                      "two dimensions are not supported"):
             Emperor(self.ord_res, self.mf, remote=False)
 
+    def test_initial_unbalanced_more_than_five(self):
+        mf = self.mf.copy()
+        mf.drop(['PC.354', 'PC.355', 'PC.356', 'PC.481', 'PC.607', 'PC.636'],
+                inplace=True)
+        with self.assertRaisesRegexp(KeyError, "There are samples not "
+                                     "included in the sample mapping file. "
+                                     "Override this error by using the "
+                                     "`ignore_missing_samples` argument. "
+                                     "Showing only the first 5 samples out of "
+                                     "6: PC.354, PC.355, PC.356, PC.481, "
+                                     "PC.607 ..."):
+            Emperor(self.ord_res, mf, remote=self.url)
+
     def test_initial_unbalanced(self):
         mf = self.mf.copy()
         mf.drop(['PC.354'], inplace=True)