The relationship between pollution level in estuarine sediment and fluctuating asymmetry (FA) of resident smooth toadfish Tetractenos glaber was evaluated. A total of 188 fish from Sydney and Hawkesbury River estuaries (5 locations from each) were analysed for 28 bilateral skull bone characters. Sediment pollution was quantified based on analysis of heavy metals (Cd, Cr, Cu, Ni, Pb and Zn) and organochlorine pesticides (DDT, DDD, DDE, chlordane, dieldrin, lindane). Sediment toxicity was characterized using the mean quotient approach (MERMQ) and ranged from low to moderate level for heavy metals and from low to severe for organochlorides. The mean shape and directional asymmetry of fish bones differed among locations, suggesting a response to local environments. FA was positively correlated with organochlorine pesticides across locations, but not with heavy metals. These results suggest that fish FA could be a useful estimator of stress caused by organic toxicity based on the MERMQ approach.