Objectives The ferredoxins are iron-sulfur proteins, which function in electron transfer reactions in a variety of systems and participate in the activation of the antimicrobial agent metronidazole. The aim of this study is to clone and characterize ferredoxin genes of Trichomonas vaginalis. Methods A cDNA expression library was constructed with T. Vaginalis total RNA. Hundreds of cDNA clones were isolated and sequenced. Sequence analysis was performed using BLAST programs, ClustalW program, etc. Results One of the cDNA clones, which has homology with T.vaginalis ferredoxin, was further analyzed. This cDNA clone has an open reading frame of 312 base pairs. The deduced precursor protein contains 103 amino acid residues with a hydrogenosome targeting sequence (MLSQCSPLRF) at the N-terminal end. The primary sequence analysis revealed that this new ferredoxin (TvFd2) has a high homology (69% identity) to the previous reported T.vaginalis ferredoxin(TvFd). Interestingly, TvFd2 is homologous to both the two subclasses of (2Fe-2S) ferredoxins, the oxidase ferredoxins and the photosynthetic ferredoxins,but with low similarity. The conserved four-cysteine residues, which are predicted to form the iron-sulfur cluster,are arranged in a typical pattern of (2Fe-2S)ferredoxins(-C-X5-C-X2-C-Xn-C-). Conclusion These data show that TvFd2 is a putative new (2Fe-2S) ferredoxin of T.vaginalis. Its biological function remains to be studied.