diff --git a/language/casper/evaluate/top_metrics.py b/language/casper/evaluate/top_metrics.py
index 3dfa432..d0e09e0 100644
--- a/language/casper/evaluate/top_metrics.py
+++ b/language/casper/evaluate/top_metrics.py
@@ -25,7 +25,14 @@ def _safe_divide(x, y):
 def top_metrics(targets: List[str],
                 predictions: List[str],
                 error_on_invalid_target: bool = True) -> Dict[str, float]:
-  """Returns eval metrics for TOP and MTOP datasets."""
+  """Returns eval metrics for TOP and MTOP datasets.
+
+  Raises:
+    ValueError: If targets and predictions contain different numbers of parses.
+  """
+  if len(targets) != len(predictions):
+    raise ValueError("Unequal number of parses: gold = {}, pred = {}".format(
+        len(targets), len(predictions)))
   num_correct = 0
   num_total = 0
   num_invalid = 0
diff --git a/language/casper/evaluate/top_metrics_test.py b/language/casper/evaluate/top_metrics_test.py
new file mode 100644
index 0000000..8bfb3b3
--- /dev/null
+++ b/language/casper/evaluate/top_metrics_test.py
@@ -0,0 +1,116 @@
+# Copyright 2026 Google LLC
+#
+# Licensed under the Apache License, Version 2.0 (the "License");
+# you may not use this file except in compliance with the License.
+# You may obtain a copy of the License at
+#
+#     https://www.apache.org/licenses/LICENSE-2.0
+#
+# Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an "AS IS" BASIS,
+# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+# See the License for the specific language governing permissions and
+# limitations under the License.
+
+"""Tests for complete, aligned TOP metric inputs."""
+
+import os
+import pathlib
+import subprocess
+import sys
+import tempfile
+
+from absl.testing import absltest, parameterized
+
+from language.casper.evaluate import top_metrics
+from language.casper.utils import top_utils
+
+_PARSE = '[IN:SET_ALARM [SL:DATE_TIME seven ] ]'
+_OTHER_VALUE = '[IN:SET_ALARM [SL:DATE_TIME eight ] ]'
+_OTHER_INTENT = '[IN:GET_WEATHER [SL:DATE_TIME tomorrow ] ]'
+
+
+class TopMetricsTest(parameterized.TestCase):
+
+  @parameterized.product(
+      sizes=[(2, 1), (1, 2), (1, 0), (0, 1)],
+      error_on_invalid_target=[False, True],
+  )
+  def test_unequal_lengths_raise(self, sizes, error_on_invalid_target):
+    targets = [_PARSE] * sizes[0]
+    predictions = [_PARSE] * sizes[1]
+    with self.assertRaisesRegex(ValueError, 'Unequal number of parses'):
+      top_metrics.top_metrics(targets, predictions, error_on_invalid_target)
+    self.assertEqual(targets, [_PARSE] * sizes[0])
+    self.assertEqual(predictions, [_PARSE] * sizes[1])
+
+  def test_mixed_predictions_keep_existing_metrics(self):
+    actual = top_metrics.top_metrics(
+        [_PARSE] * 4, [_PARSE, _OTHER_VALUE, _OTHER_INTENT, 'invalid']
+    )
+    self.assertEqual(actual, {
+        'num_total': 4, 'full_accuracy': 0.25, 'intent_accuracy': 0.5,
+        'intent_arg_accuracy': 0.5, 'invalid_predictions': 0.25,
+    })
+
+  def test_matching_empty_inputs(self):
+    self.assertEqual(top_metrics.top_metrics([], []), {
+        'num_total': 0, 'full_accuracy': 0.0, 'intent_accuracy': 0.0,
+        'intent_arg_accuracy': 0.0, 'invalid_predictions': 0.0,
+    })
+
+  @parameterized.parameters(list, tuple)
+  def test_aligned_sequences(self, sequence_type):
+    values = sequence_type([_PARSE, _OTHER_INTENT])
+    result = top_metrics.top_metrics(values, values)
+    self.assertEqual(result, {
+        'num_total': 2, 'full_accuracy': 1.0, 'intent_accuracy': 1.0,
+        'intent_arg_accuracy': 1.0, 'invalid_predictions': 0.0,
+    })
+
+  def test_formatted_prediction_has_the_same_frame(self):
+    result = top_metrics.top_metrics(
+        [_PARSE], [top_utils.format_serialized(_PARSE)]
+    )
+    self.assertEqual(result['full_accuracy'], 0.0)
+    self.assertEqual(result['intent_accuracy'], 1.0)
+    self.assertEqual(result['intent_arg_accuracy'], 1.0)
+
+  def test_invalid_target_still_raises_when_requested(self):
+    with self.assertRaises(AssertionError):
+      top_metrics.top_metrics(['invalid'], [_PARSE])
+
+  def test_invalid_target_policy_is_unchanged(self):
+    result = top_metrics.top_metrics(
+        ['invalid', _PARSE], [_PARSE, _PARSE], error_on_invalid_target=False
+    )
+    self.assertEqual(result['num_total'], 2)
+    self.assertEqual(result['full_accuracy'], 0.5)
+    self.assertEqual(result['intent_accuracy'], 0.5)
+    self.assertEqual(result['intent_arg_accuracy'], 0.5)
+
+  @parameterized.parameters(True, False)
+  def test_existing_cli_alignment_check(self, aligned):
+    with tempfile.TemporaryDirectory() as directory:
+      gold = pathlib.Path(directory) / 'gold.tsv'
+      pred = pathlib.Path(directory) / 'pred.tsv'
+      gold.write_text('query\t' + _PARSE + '\n', encoding='utf-8')
+      pred.write_text((_PARSE + '\n') if aligned else '', encoding='utf-8')
+      proc = subprocess.run([
+          sys.executable, '-m',
+          'language.casper.evaluate.evaluate_mtop_predictions',
+          '--gold_file=' + str(gold), '--pred_file=' + str(pred),
+          '--alsologtostderr',
+      ], capture_output=True, text=True, timeout=60, check=False,
+          env=os.environ.copy())
+    if aligned:
+      self.assertEqual(proc.returncode, 0, proc.stderr)
+      self.assertIn('Exact match accuracy: 100.00', proc.stderr)
+    else:
+      self.assertNotEqual(proc.returncode, 0)
+      self.assertIn('Unequal number of parses', proc.stderr)
+      self.assertNotIn('Exact match accuracy:', proc.stderr)
+
+
+if __name__ == '__main__':
+  absltest.main()