diff --git a/conftest.py b/conftest.py
index a1ab2aed5..ec975c428 100644
--- a/conftest.py
+++ b/conftest.py
@@ -5,6 +5,7 @@
 from olmo.config import (
     DataConfig,
     InitFnType,
+    InstanceFilterConfig,
     ModelConfig,
     OptimizerConfig,
     PaddingDirection,
@@ -72,6 +73,9 @@ def train_config(tmp_path, model_config) -> TrainConfig:
                 "test_fixtures/c4-sample.03.json.gz",
             ],
             pad_direction=PaddingDirection.right,
+            instance_filter=InstanceFilterConfig(
+                repetition_max_period=3, repetition_min_period=1, repetition_max_count=3
+            ),
         ),
         tokenizer=TokenizerConfig(identifier=TEST_MODEL),
         save_folder=str(tmp_path / "checkpoints"),
diff --git a/tests/data/collator_test.py b/tests/data/collator_test.py
index e94451313..9c3b60f29 100644
--- a/tests/data/collator_test.py
+++ b/tests/data/collator_test.py
@@ -129,3 +129,20 @@ def test_collate_with_label_mask(train_config, pad_direction):
                 [[True, False, True, True], [False, True, True, False]],
             )
         ).all()
+
+
+@pytest.mark.parametrize(
+    "pad_direction",
+    [pytest.param(PaddingDirection.right, id="pad-right"), pytest.param(PaddingDirection.left, id="pad-left")],
+)
+def test_collate_with_instance_filter(train_config, pad_direction):
+    train_config.data.pad_direction = pad_direction
+    collator = DataCollator.from_train_config(train_config)
+
+    inputs = [torch.tensor([0, 0, 2, 3]), torch.tensor([1, 1, 1])]
+    batch = collator(inputs)
+    assert batch["input_ids"].shape == (2, 4)
+    if pad_direction == "right":
+        assert batch["input_ids"][1][-1] == train_config.model.pad_token_id
+    else:
+        assert batch["input_ids"][1][0] == train_config.model.pad_token_id
diff --git a/tests/data/memmap_dataset_test.py b/tests/data/memmap_dataset_test.py
index e267043ee..39579cef1 100644
--- a/tests/data/memmap_dataset_test.py
+++ b/tests/data/memmap_dataset_test.py
@@ -3,6 +3,7 @@
 
 import numpy as np
 
+from olmo.config import InstanceFilterConfig
 from olmo.data.memmap_dataset import MemMapDataset
 from olmo.tokenizer import Tokenizer
 
@@ -106,3 +107,21 @@ def test_concat_mmap_datasets(tmp_path: Path):
     # Should get the same with negative index.
     assert ds[-1]["input_ids"].tolist() == [3, 4, 5]
     assert ds[-1]["metadata"]["label"] == "test2"
+
+
+def test_instance_filter(tmp_path: Path):
+    # Write some bad data to disk.
+    mmap = np.memmap(tmp_path / "bad_tokens.npy", dtype=np.uint16, mode="w+", shape=(128,))
+    mmap[:] = list(np.ones(31)) + list(range(64 - 31)) + list(np.ones(32)) + list(range(64 - 32))
+    mmap.flush()
+
+    instance_filter_config = InstanceFilterConfig(
+        repetition_min_period=1, repetition_max_period=13, repetition_max_count=32
+    )
+    ds = MemMapDataset(tmp_path / "bad_tokens.npy", chunk_size=64, instance_filter_config=instance_filter_config)
+
+    out = ds[0]
+    assert out["instance_mask"] is True
+
+    out = ds[1]
+    assert out["instance_mask"] is False