Benzo[a]pyrene (B[a]P) is an ubiquitous environmental carcinogen produced during incomplete combustion of organic substances. Anti-benzo[a]pyrene-7,8-dihydrodiol-9,10-epoxide (BPDE), is the most carcinogenic form of the ultimate metabolites of B[a]P. The goal of this study was to investigate the responses of human amniotic epithelial FL cells to BPDE at different time intervals after exposure and to find potential biomarkers involved in these responses. Cells were treated with 0.05 microM BPDE for 2 h and incubated for another 3, 12, and 24 h to obtain protein extracts which were resolved by 2-DE and visualized by silver staining. Sixty-four spots were up-regulated while 66 were down-regulated following BPDE exposure. These altered spots were excised from the gels and analyzed by MALDI-TOF-MS. The analysis led to the identification of 84 proteins affected by BPDE. These proteins were involved in regulation of transcription, cell cycle, apoptosis, transport, signal transduction, metabolism,and so forth. Among them, subunits of eukaryotic translation initiation factor 3 (EIF3) including EIF3S2, EIF3S3, EIF3S12, and EIF5A, component proteins of ubiquitin-proteasome system (ubiquitin carboxyl-terminal esterase L3, proteasome beta 4 subunit, and proteasome beta 3 subunit) and 14-3-3 proteins (14-3-3 zeta and epsilon) have not been previously associated with a response to BPDE exposure. All these results aid our understanding of the mechanism of BPDE induced cell defensive responses and hazardous effects as well as providing the possibility of the establishment of potential biomarkers.