This study was conceived to investigate what are the main effects of an androgen masculinizing treatment on gonadal gene expression profiles in the rainbow trout during sex differentiation. Using microarrays we characterized a highly deregulated expression profile in female treated with androgens with a clear inhibition of the female specific gene expression patterns. This suggests that androgens may acts mainly through the inhibition of female development rather than through a direct stimulatory effect on testicular differentiation.