Many basic cellular processes are shared across vast phylogenetic distances, whereas sex-determining mechanisms are highly variable between phyla, although the existence of two sexes is nearly universal in the animal kingdom. However, the evolutionarily conserved DMRT1/dsx/mab3 with a common zinc finger-like DNA-binding motif, DM domain, share both similar structure and function between phyla. Here we report that six transcripts of the chicken DMRT1 were generated in gonads by multiple alternative splicing. By cDNA cloning and genomic structure analysis, we found that there were nine exons of DMRT1, which were involved in alternatively splicing to generate the DMRT1 transcripts. Northern blotting and reverse transcription (RT) PCR analysis revealed that the expression of chicken DMRT1 was testis-specific in adults. Whole-mount in situ hybridizations and RT-PCR indicated that DMRT1 b was specially expressed in embryo gonads and higher in male than female gonads at stage 31. The female gonad had stronger DMRT1 c expression than the male one, whereas DMRT1 f was detectable only in the male gonad at stage 31 of the key time of sex gonadal differentiation. The differential expression of these transcripts during gonadal differentiation provides new insight into roles of alternative splicing of DMRT1 in governing sex differentiation of the chicken.