The release of produced water (PW), a by-product of offshore oil production, has increased in Norwegian waters in recent years. Alkylphenols (AP), a major component of PW, have been shown to have endocrine disrupting effects on several fish species. In the present study, four groups of female Atlantic cod (Gadus morhua) were orally exposed for 20 weeks to two different concentrations of a mixture of C4-C7 APs, PW or 17beta-estradiol. The transcriptional responses in the liver of Atlantic female cod were studied using a custom-made cDNA microarray. The largest transcriptional effects were seen in cod exposed to the lowest dose of APs. Several biological processes such as glycolysis, apoptosis and the general stress response were affected by exposure to APs. In addition, genes coding for the detoxification enzymes CYP1A and sulfotransferase 2 were up-regulated in the low exposure group. Significant reduction in gonadosomatic index (GSI) and the concentration of plasma vitellogenin were seen in both AP and 17beta-estradiol exposed cod. Exposure to PW had little effect on GSI and the regulation of stress responsive genes. The findings indicate that chronic exposure to low levels of APs may cause a stress response and delayed maturation in female cod.