To identify a sensitive biomarker of freshwater monitoring, we evaluated pollutant-induced expression of heat shock proteins (HSPs) and hemoglobins (Hbs) genes in the larvae of the aquatic midge Chironomus tentans (Diptera, Chironomidae). As pollutants, we examined nonylphenol, bisphenol-A, 17alpha-ethynyl estradiol, bis(2-ethylhexyl) phthalate, endosulfan, paraquat dichloride, chloropyriphos, fenitrothion, cadmium chloride, lead nitrate, potassium dichromate, benzo[a]pyrene and carbon tetrachloride. We also investigated larval growth as a physiological descriptor by measuring changes in the body fresh weight and dry weight after chemical exposure. The response of the HSPs gene expression by chemical exposure was rapid and sensitive to low chemical concentrations but it was not stressor specific. Interestingly, an increase in the expression of HSPs genes was observed not only in a stress inducible form (HSP70), but also in a constitutively (HSC70) expressed form. The expression of Hb genes showed chemical-specific responses: that is, alkyl phenolic compounds increased the expression of hemoglobin genes, whereas pesticides decreased the expression. As expected, molecular-level markers were more sensitive than physiological endpoints, suggesting that gene expression could be developed as an early warning biomarker in this animal. The overall results suggest that the expression of HSP and Hb genes in Chironomus could give useful information for diagnosing general health conditions in fresh water ecosystem. The expression of Hb genes, in particular, seems to be a promising biomarker, especially in view of the potential of Chironomus larvae as a biomonitoring species and of the physiological particularities of their respiratory pigments.