diff --git a/doc/source/whatsnew/v0.19.0.txt b/doc/source/whatsnew/v0.19.0.txt
index 58a92cfa5a784..f24bbe8e52ec8 100644
--- a/doc/source/whatsnew/v0.19.0.txt
+++ b/doc/source/whatsnew/v0.19.0.txt
@@ -728,3 +728,5 @@ Bug Fixes
 - Bug where ``pd.read_gbq()`` could throw ``ImportError: No module named discovery`` as a result of a naming conflict with another python package called apiclient  (:issue:`13454`)
 - Bug in ``Index.union`` returns an incorrect result with a named empty index (:issue:`13432`)
 - Bugs in ``Index.difference`` and ``DataFrame.join`` raise in Python3 when using mixed-integer indexes (:issue:`13432`, :issue:`12814`)
+
+- Bug in ``MultiIndex.from_arrays`` didn't check for input array lengths (:issue:`13599`)
diff --git a/pandas/indexes/multi.py b/pandas/indexes/multi.py
index 365a971f82a3b..184744915bd8d 100644
--- a/pandas/indexes/multi.py
+++ b/pandas/indexes/multi.py
@@ -848,6 +848,12 @@ def from_arrays(cls, arrays, sortorder=None, names=None):
             name = None if names is None else names[0]
             return Index(arrays[0], name=name)
 
+        # Check if lengths of all arrays are equal or not,
+        # raise ValueError, if not
+        for i in range(1, len(arrays)):
+            if len(arrays[i]) != len(arrays[i - 1]):
+                raise ValueError('all arrays must be same length')
+
         cats = [Categorical.from_array(arr, ordered=True) for arr in arrays]
         levels = [c.categories for c in cats]
         labels = [c.codes for c in cats]
diff --git a/pandas/tests/indexes/test_multi.py b/pandas/tests/indexes/test_multi.py
index 2734e90a1971b..5597e1ffa8c87 100644
--- a/pandas/tests/indexes/test_multi.py
+++ b/pandas/tests/indexes/test_multi.py
@@ -632,6 +632,27 @@ def test_from_arrays_index_series_period(self):
 
         tm.assert_index_equal(result, result2)
 
+    def test_from_arrays_different_lengths(self):
+        # GH13599
+        idx1 = [1, 2, 3]
+        idx2 = ['a', 'b']
+        assertRaisesRegexp(ValueError, '^all arrays must be same length$',
+            MultiIndex.from_arrays, [idx1, idx2])
+
+    def test_from_arrays_different_lengths_first_array_zero_length(self):
+        # GH13599
+        idx1 = []
+        idx2 = ['a', 'b']
+        assertRaisesRegexp(ValueError, '^all arrays must be same length$',
+            MultiIndex.from_arrays, [idx1, idx2])
+
+    def test_from_arrays_different_lengths_second_array_zero_length(self):
+        # GH13599
+        idx1 = [1, 2, 3]
+        idx2 = []
+        assertRaisesRegexp(ValueError, '^all arrays must be same length$',
+            MultiIndex.from_arrays, [idx1, idx2])
+
     def test_from_product(self):
 
         first = ['foo', 'bar', 'buz']