A semi-nested reverse transcriptase-polymerase chain reaction (RT-PCR) was applied to evaluate the presence of estrogen receptor-alpha (ER-alpha) in human prostate cancer cells. Unexpectedly, a novel fatty acid synthase (FAS)/ER-alpha fusion transcript was identified, in which the N-terminus of FAS was fused in-frame with the C-terminus of ER-alpha. The existence of the FAS/ER-alpha transcript was further confirmed by RT-PCR analysis using various sets of amplification primers and different reverse-transcribed primers in the presence of dimethyl sulfoxide to eliminate the secondary structure of RNA. The predicted FAS/ER-alpha protein would contain largely domain I of FAS and the entire ligand binding domain of ER-alpha. The FAS/ER-alpha was expressed in a variety of human cancer cell lines including prostate, breast, cervical and bladder cancer cell lines. Our data suggest that the presence of FAS/ER-alpha may complicate the FAS and the ER-alpha signalling pathway.