diff --git a/src/grelu/lightning/__init__.py b/src/grelu/lightning/__init__.py
index 7159fde..1ae19e8 100644
--- a/src/grelu/lightning/__init__.py
+++ b/src/grelu/lightning/__init__.py
@@ -676,6 +676,24 @@ def tune_on_dataset(
         """
         # Move train data parameters
         self.base_data_params = self.data_params.copy()
+
+        # Warn if fine-tuning chromosomes overlap with pretraining chromosomes
+        base_intervals = self.base_data_params.get("train", {}).get("intervals")
+        if (
+            base_intervals is not None
+            and hasattr(train_dataset, "intervals")
+            and train_dataset.intervals is not None
+        ):
+            base_chroms = set(base_intervals["chrom"])
+            new_chroms = set(train_dataset.intervals["chrom"])
+            overlap = sorted(base_chroms & new_chroms)
+            if overlap:
+                warnings.warn(
+                    f"Fine-tuning dataset contains {len(overlap)} chromosome(s) "
+                    f"({', '.join(overlap)}) that overlap with the pretrained "
+                    "model's training data. This may lead to data leakage."
+                )
+
         self.data_params = {}
 
         # Make new model head
diff --git a/tests/test_lightning.py b/tests/test_lightning.py
index d734ba7..7bc9e19 100644
--- a/tests/test_lightning.py
+++ b/tests/test_lightning.py
@@ -1,3 +1,5 @@
+import warnings
+
 import numpy as np
 import pandas as pd
 import torch
@@ -344,6 +346,38 @@ def test_lightning_model_finetune():
     assert multitask_reg_model.model_params["n_tasks"] == 1
 
 
+def test_lightning_model_finetune_chrom_overlap_warning():
+    """Warn when fine-tuning chromosomes overlap with pretraining chromosomes."""
+    model = generate_model(task="regression", loss="poisson", n_tasks=2)
+    # Simulate a pretrained model that was trained on chr1
+    model.data_params["train"] = {
+        "intervals": {"chrom": ["chr1", "chr1"], "start": [0, 100], "end": [2, 102]},
+        "seq_len": 2,
+    }
+
+    # Fine-tune with interval_dataset which also uses chr1
+    with warnings.catch_warnings(record=True) as w:
+        warnings.simplefilter("always")
+        model.tune_on_dataset(
+            interval_dataset, interval_dataset, final_pool_func="avg"
+        )
+        overlap_warnings = [x for x in w if "overlap" in str(x.message)]
+        assert len(overlap_warnings) == 1
+        assert "chr1" in str(overlap_warnings[0].message)
+        assert "data leakage" in str(overlap_warnings[0].message)
+
+
+def test_lightning_model_finetune_no_chrom_warning():
+    """No warning when fine-tuning with non-interval datasets."""
+    model = generate_model(task="regression", loss="poisson", n_tasks=2)
+    # ldataset is string-based (no intervals), so no warning should fire
+    with warnings.catch_warnings(record=True) as w:
+        warnings.simplefilter("always")
+        model.tune_on_dataset(ldataset, ldataset, final_pool_func="avg")
+        overlap_warnings = [x for x in w if "overlap" in str(x.message)]
+        assert len(overlap_warnings) == 0
+
+
 def test_lightning_model_ensemble():
     # Make individual models
     model0 = generate_model(task="binary", loss="bce", n_tasks=2)