Intersexuality has been found in both males and females of the marine/estuarine amphipod, Echinogammarus marinus, at polluted and reference sites in East Scotland. Polluted sites had significantly more intersex specimens than reference sites, however the cause of intersexuality is unclear. Discriminant analysis of morphometric data showed that normal male specimens from the most polluted site resembled pooled intersex males, suggesting that subtle endocrine disruption (ED) maybe occurring in these otherwise apparently normal males. The main discriminating character was gnathopod size, recognised to be under androgenic gland control. The association of distinctive morphometry with intersexuality may provide a new approach to biomarkers of ED in crustaceans. The opportunities for other novel biomarkers, for example biochemical or behavioural markers, may also be explored through study of intersex animals.