Chemical pollution of the aquatic environment is almost always the result of multiple rather than single toxic compounds. The possibility of separating the effects of key risk chemicals from those of others, including theirjoint effects, is of clear theoretical interest and high technical importance. We addressed this goal using multiple gene expression profiling in the liver of juvenile brown trout (Salmo trutta lacustris) exposed to three model chemicals (cadmium, carbon tetrachloride [CCl4], and pyrene) administered singly, in binary and trinary combinations at low acutely sublethal concentrations, and in the partial dose-response manner. Differentially expressed genes were grouped by correlation of profiles, and the dependence on dose was analyzed with multiple regression. Responses to cadmium and CCl4 were largely similar, and no sign of interaction was observed (i.e., in binary combinations, the effects were equal to those produced by the more potent compound, cadmium). Joint effects became apparent in the presence of pyrene, which caused markedly different alterations in gene expression. Using the results of 118 experiments conducted earlier for comparison, we found a group of 23 genes responding to chemical toxicity (cadmium, CCl4, pyrene, and resin acids) with significantly higher probability than that of responding to other stressors (handling or viral and bacterial infections). This group included genes implicated in the immune and stress responses that were markedly enriched in extracellular proteins. In conclusion, we demonstrated that chemical-characteristic genomic endpoints often remain when the chemical is present as part of a binary or a trinary mixture. Despite dissimilar chemistry and different cellular targets, the degree of responses to the combination of cadmium and CCl4 appeared to be less than additive. Chemical interactions or nonadditive effects manifested when a compound with a markedly different mode of action (pyrene) was included into the mixture.