diff --git a/datapipe/sql_util.py b/datapipe/sql_util.py
index 1a7495a1..94a4dfd3 100644
--- a/datapipe/sql_util.py
+++ b/datapipe/sql_util.py
@@ -1,5 +1,6 @@
 from typing import Any, Dict, List, Optional
 
+import pandas as pd
 from sqlalchemy import Column, Integer, String, Table, tuple_
 
 from datapipe.run_config import RunConfig
@@ -21,9 +22,17 @@ def sql_apply_idx_filter_to_table(
         # Когда ключей много - сравниваем по кортежу
         keys = tuple_(*[table.c[key] for key in primary_keys])  # type: ignore
 
-        sql = sql.where(
-            keys.in_([tuple([r[key] for key in primary_keys]) for r in idx.to_dict(orient="records")])  # type: ignore
-        )
+        where_values: list[tuple] = []
+        for r in idx.to_dict(orient="records"):
+            this_row: list[Any] = []
+            for key in primary_keys:
+                if pd.isna(r[key]):
+                    this_row.append(None)
+                else:
+                    this_row.append(r[key])
+            where_values.append(tuple(this_row))
+
+        sql = sql.where(keys.in_(where_values))
 
     return sql
 
diff --git a/datapipe/store/tests/abstract.py b/datapipe/store/tests/abstract.py
index d5a64d76..50faa4c1 100644
--- a/datapipe/store/tests/abstract.py
+++ b/datapipe/store/tests/abstract.py
@@ -6,7 +6,7 @@
 import cloudpickle
 import pandas as pd
 import pytest
-from sqlalchemy import Column, String
+from sqlalchemy import Column, Integer, String
 
 from datapipe.run_config import RunConfig
 from datapipe.store.table_store import TableStore
@@ -49,6 +49,47 @@ def test_get_schema(
 
         assert store.get_schema() == schema
 
+    def test_multiple_keys_with_nan(self, store_maker: TableStoreMaker) -> None:
+        data_df = pd.DataFrame(
+            {
+                "id1": [1, 2, 3],
+                "id2": ["a", "b", "c"],
+                "value": [10, 20, 30],
+            }
+        )
+        schema: list[Column] = [
+            Column("id1", Integer, primary_key=True),
+            Column("id2", String(100), primary_key=True),
+            Column("value", Integer),
+        ]
+
+        store = store_maker(schema)
+        store.insert_rows(data_df)
+
+        assert_df_equal(
+            store.read_rows(
+                data_to_index(
+                    pd.DataFrame.from_dict({"id1": [2, -1], "id2": ["b", None]}),
+                    ["id1", "id2"],
+                )
+            ),
+            pd.DataFrame.from_dict({"id1": [2], "id2": ["b"], "value": [20]}),
+            index_cols=["id1", "id2"],
+        )
+
+        assert_df_equal(
+            store.read_rows(
+                data_to_index(
+                    pd.DataFrame.from_dict({"id1": [2, None], "id2": ["b", "z"]}),
+                    ["id1", "id2"],
+                )
+            ),
+            pd.DataFrame.from_dict({"id1": [2], "id2": ["b"], "value": [20]}),
+            index_cols=["id1", "id2"],
+        )
+
+        assert_ts_contains(store, data_df)
+
     @pytest.mark.parametrize("data_df,schema", DATA_PARAMS)
     def test_write_read_rows(
         self,