diff --git a/jax/_src/nn/functions.py b/jax/_src/nn/functions.py
index b49e16d95408..a5b5aaf31799 100644
--- a/jax/_src/nn/functions.py
+++ b/jax/_src/nn/functions.py
@@ -786,10 +786,14 @@ def _get_causal_mask(T, S):
   return mask[None, None, :, :]
 
 def _get_padding_mask_logits(T, S, q_seqlen, kv_seqlen):
-  q_indices = jnp.arange(0, T)[None, :, None]
-  kv_indices = jnp.arange(0, S)[None, None, :]
-  q_mask = q_indices < q_seqlen[:, None, None]
-  kv_mask = kv_indices < kv_seqlen[:, None, None]
+  q_mask = True
+  kv_mask = True
+  if q_seqlen is not None:
+    q_indices = jnp.arange(0, T)[None, :, None]
+    q_mask = q_indices < q_seqlen[:, None, None]
+  if kv_seqlen is not None:
+    kv_indices = jnp.arange(0, S)[None, None, :]
+    kv_mask = kv_indices < kv_seqlen[:, None, None]
   mask = jnp.logical_and(q_mask, kv_mask)
   return mask[:, None, :, :]
 
@@ -813,7 +817,7 @@ def _apply_masks(logits, mask, is_causal, q_seqlen, kv_seqlen):
     mask = _get_causal_mask(T, S)
     combined_mask = jnp.logical_and(combined_mask, mask)
 
-  if q_seqlen is not None and kv_seqlen is not None:
+  if q_seqlen is not None or kv_seqlen is not None:
     mask = _get_padding_mask_logits(T, S, q_seqlen, kv_seqlen)
     combined_mask = jnp.logical_and(combined_mask, mask)
 
@@ -1001,12 +1005,22 @@ def _check_shape_and_dtype(t: Array | None, shape: Sequence[int],
           kv_seqlen=key_value_seq_lengths,
       )
     case 'cudnn':
+      use_padding = (
+           query_seq_lengths is not None or key_value_seq_lengths is not None
+      )
+      if use_padding:
+        if query_seq_lengths is None:
+          T = query_arr.shape[1]
+          query_seq_lengths = jnp.full((B,), T, dtype=jnp.int32)
+        if key_value_seq_lengths is None:
+          key_value_seq_lengths = jnp.full((B,), S, dtype=jnp.int32)
+
       mask_type = MaskType.NO_MASK
-      if query_seq_lengths is not None and is_causal:
+      if use_padding and is_causal:
         mask_type = MaskType.PADDING_CAUSAL
       elif is_causal:
         mask_type = MaskType.CAUSAL
-      elif query_seq_lengths is not None:
+      elif use_padding:
         mask_type = MaskType.PADDING
       out = cudnn_dot_product_attention(
           query_arr, key_arr, value_arr, bias, mask, query_seq_lengths,