Biliary polycyclic aromatic hydrocarbon (PAH) and alkylphenol (AP) metabolites, hepatic gene expression, and corresponding enzyme activities were determined in the deep-sea fish Alepocephalus rostratus from two sites within the Mediterranean. Biliary metabolites included the hydroxylated PAH metabolites (OH-PAHs) 1-naphthol, 2-naphthol, 9-fluorenol, 9-phenanthrol, and 1-pyrenol and the APs 4-nonylphenol (NP) and 4-tert-octylphenol (OP). Five biomarker genes, namely, cytochrome P450 1A (CYP1A), vitellogenin (Vtg), catalase (CAT), Cu/Zn-superoxide-dismutase (Cu/Zn-SOD), and glutathione reductase (GR), were quantified using qRT-PCR. Moreover, corresponding enzyme activities (ethoxyresorufin-O-deethylase (EROD), CAT, SOD, and GR) were also determined. The ΣOH-PAHs detected ranged from 21.1 to 300.3 ng/g bile and were mainly composed of 1-naphthol. Both NP and OP metabolites were detected in all samples with concentrations ranging from 17.4 to 107.2 ng/g bile and 4.9 to 17.3 ng/g bile, respectively, and levels were significantly higher in samples from the western Mediterranean (WM) compared to those from the Catalan slope (CS). Accordingly, gene expression was significantly induced in male fish from the WM; however, these results were not reflected in enzyme activity levels. In particular, males caught at 2000 m in the WM exhibited 35-times higher Vtg levels compared to those from the CS, suggesting that endocrine-disrupting effects may potentially be occurring in such remote environments as the deep-sea.