Metal effects on Ruditapes philippinarum were assessed using aneuploidy as cytogenetic endpoint.

Clam aneuploidy was generally related to sediment contamination but not to metal bioaccumulation.

Chronic metal contamination may be inducing long-term clam aneuploidy levels.

Vertical transmission hypothesis is suggested for the high aneuploidy levels under chronic contamination.

Aneuploidy represents an effective tool to detect long-term metal effects on estuarine bivalves.