Shellfish may bioaccumulate a variety of chemicals, some of which are mutagenic or carcinogenic to humans. Mutagenicity tests provide an integrated way of detecting these chemicals. This paper describes the application of two such tests to New Zealand shellfish in laboratory and field situations. The bacterial mutagenicity test gave positive results on a nitric acid extract of green‐lipped mussels (Perna canaliculus) that had been exposed to model carcinogens under laboratory conditions. When applied to Pacific oysters (Crassostrea gigas) that had been sampled from four different sites in the Manukau Harbour, the same methods detected mutagenic activity which varied both by date and area sampled. The micronucleus assay gave a readily scored measure of chromosome damage in gill tissues in both mussels and oysters, but presented some practical problems in field studies. Our studies emphasise the need to sample within a short time interval, and the advantage of using a complementary package of bacterial mutagenicity and gill micronucleus assays.