diff --git a/sgkit/io/vcf/vcf_reader.py b/sgkit/io/vcf/vcf_reader.py
index f1da036d3..c66a00db2 100644
--- a/sgkit/io/vcf/vcf_reader.py
+++ b/sgkit/io/vcf/vcf_reader.py
@@ -525,6 +525,10 @@ def vcf_to_zarr_sequential(
             ds.attrs["filters"] = filters
             ds.attrs["vcf_zarr_version"] = "0.1"
             ds.attrs["vcf_header"] = vcf.raw_header
+            try:
+                ds.attrs["contig_lengths"] = vcf.seqlens
+            except AttributeError:
+                pass
 
             for field_handler in field_handlers:
                 field_handler.update_dataset(ds)
diff --git a/sgkit/tests/io/vcf/test_vcf_reader.py b/sgkit/tests/io/vcf/test_vcf_reader.py
index 661b5f2fe..eb5483fed 100644
--- a/sgkit/tests/io/vcf/test_vcf_reader.py
+++ b/sgkit/tests/io/vcf/test_vcf_reader.py
@@ -32,6 +32,7 @@ def test_vcf_to_zarr__small_vcf(shared_datadir, is_path, tmp_path):
     ds = xr.open_zarr(output)
 
     assert ds.attrs["contigs"] == ["19", "20", "X"]
+    assert "contig_lengths" not in ds.attrs
     assert_array_equal(ds["variant_contig"], [0, 0, 1, 1, 1, 1, 1, 1, 2])
     assert_array_equal(
         ds["variant_position"],
@@ -155,6 +156,8 @@ def test_vcf_to_zarr__large_vcf(shared_datadir, is_path, tmp_path):
     vcf_to_zarr(path, output, chunk_length=5_000)
     ds = xr.open_zarr(output)
 
+    assert ds.attrs["contigs"] == ["20", "21"]
+    assert ds.attrs["contig_lengths"] == [63025520, 48129895]
     assert ds["sample_id"].shape == (1,)
     assert ds["call_genotype"].shape == (19910, 1, 2)
     assert ds["call_genotype_mask"].shape == (19910, 1, 2)
diff --git a/sgkit/tests/io/vcf/test_vcf_roundtrip.py b/sgkit/tests/io/vcf/test_vcf_roundtrip.py
index 7f591857c..e0c628688 100644
--- a/sgkit/tests/io/vcf/test_vcf_roundtrip.py
+++ b/sgkit/tests/io/vcf/test_vcf_roundtrip.py
@@ -199,6 +199,9 @@ def test_all_fields(
     assert allel_ds_contigs <= sg_ds_contigs
     del allel_ds.attrs["contigs"]
     del sg_ds.attrs["contigs"]
+    # scikit-allel doesn't store contig lengths
+    if "contig_lengths" in sg_ds.attrs:
+        del sg_ds.attrs["contig_lengths"]
 
     if allel_ds_contigs < sg_ds_contigs:
         # variant_contig variables are not comparable, so remove them before comparison