diff --git a/CHANGELOG.rst b/CHANGELOG.rst
index 83cad0b5..b67fd7cc 100644
--- a/CHANGELOG.rst
+++ b/CHANGELOG.rst
@@ -9,6 +9,9 @@ Changelog
 
 version 1.10.0-dev
 ------------------
++ Fix ``python -m isal.igzip`` replacing the input file with empty output and
+  exiting with status 0 when the output file is the input file, as in
+  ``-f -o data data``. It exits with an error now.
 + Speed up ``import isal.igzip`` and ``import isal.igzip_threaded`` by not
   importing ``typing``.
 + Fix the gzip header that ``igzip_threaded.open`` writes when ``threads`` is
diff --git a/src/isal/igzip.py b/src/isal/igzip.py
index a7a2d5a5..1c188a7e 100644
--- a/src/isal/igzip.py
+++ b/src/isal/igzip.py
@@ -349,6 +349,11 @@ def main():
             if extension != ".gz" and not args.stdout:
                 sys.exit(f"filename doesn't end in .gz: {args.file!r}. "
                          f"Cannot determine output filename.")
+    # Opening the output for writing would empty the input before it is read.
+    if (args.file is not None and out_filepath is not None
+            and os.path.exists(args.file) and os.path.exists(out_filepath)
+            and os.path.samefile(args.file, out_filepath)):
+        sys.exit(f"{args.file!r} and {out_filepath!r} are the same file")
     if out_filepath is not None and not args.force:
         if os.path.exists(out_filepath):
             yes_or_no = input(f"{out_filepath} already exists; "
diff --git a/tests/test_igzip.py b/tests/test_igzip.py
index 62ca42e2..1c691c2b 100644
--- a/tests/test_igzip.py
+++ b/tests/test_igzip.py
@@ -355,6 +355,29 @@ def test_compress_infile_out_file_force(monkeypatch, tmp_path, capsysbinary):
     assert out == b''
 
 
+@pytest.mark.parametrize("args", [
+    ['-f', '-o', 'test', 'test'],
+    ['-f', '-o', os.path.join('.', 'test'), 'test'],
+    ['-o', 'test', 'test'],  # Refused before the overwrite prompt.
+    ['-d', '-f', '-o', 'test.gz', 'test.gz'],
+])
+def test_infile_out_file_same_file(monkeypatch, tmp_path, capsysbinary, args):
+    monkeypatch.chdir(tmp_path)
+    test = tmp_path / "test"
+    test.write_bytes(DATA)
+    test_gz = tmp_path / "test.gz"
+    test_gz.write_bytes(COMPRESSED_DATA)
+    monkeypatch.setattr(sys, "argv", ['', *args])
+    monkeypatch.setattr(sys, "stdin", io.TextIOWrapper(io.BytesIO(b"y")))
+    with pytest.raises(SystemExit) as error:
+        igzip.main()
+    assert error.match("are the same file")
+    assert test.read_bytes() == DATA
+    assert test_gz.read_bytes() == COMPRESSED_DATA
+    out, err = capsysbinary.readouterr()
+    assert out == b''
+
+
 def test_compress_infile_out_file_prompt(monkeypatch, tmp_path, capsysbinary):
     test = tmp_path / "test"
     test.write_bytes(DATA)