diff --git a/cytetype/preprocessing/extraction.py b/cytetype/preprocessing/extraction.py
index 44f9c9c..693a451 100644
--- a/cytetype/preprocessing/extraction.py
+++ b/cytetype/preprocessing/extraction.py
@@ -78,12 +78,26 @@ def extract_marker_genes(
             gene_ids_to_name[gene] for gene in top_genes if gene in gene_ids_to_name
         ]
 
+        lost_genes = len(top_genes) - len(markers[cluster_id])
+        if lost_genes > 0:
+            logger.warning(
+                f"Number of lost genes ({lost_genes}) for group '{group_name}' (cluster '{cluster_id}'). \n"
+                f"This could indicate inconsistencies with the marker genes and the genes in adata.var."
+            )
+
     if not any_genes_found:
         raise ValueError(
             "No marker genes found for any group. This could indicate issues with the "
             "rank_genes_groups analysis or that all groups have insufficient marker genes."
         )
 
+    if not any(markers.values()):
+        raise ValueError(
+            "All marker gene lists are empty. Gene names in rank_genes_groups "
+            "could not be matched to adata.var_names. This typically happens "
+            "when var_names were changed after rank_genes_groups was run."
+        )
+
     return markers