We study the molecular regulation of sex in cyprinids, with special emphasis on male gonad differentiation by using the tools of comparative and functional genomics. We have clustered nearly 60 thousand gonad-derived zebrafish ESTs to yield over 6500 ¿Gonad Uniclone¿ sequences (over 1500 unique to our collection). Inserts of these selected clones were printed onto slides to produce the first gonad-derived cDNA microarray from zebrafish. Labeled RNAs from adult and differentiating gonads were hybridized onto the array to identify differentially expressed genes. Several of these genes are novel and conserved among vertebrates, the preliminary analysis of a selected set together with candidate genes will be presented. The development of vasegfp transgenic individuals (from Lisbeth Olsen, Bergen, Norway) was followed by detecting the level of EGFP expression in their gonads. Samples collected at selected time points were subjected to histological analysis. Our data indicate that all zebrafish males go through an ovary-to-testis transformation, however variable starting time and wide-ranging levels of EGFP expression in ¿juvenile ovaries¿ yield a complex picture even among siblings. Differentiating testis samples were isolated from monosex common carp individuals produced by crossing YY ¿supermale¿ individuals with XX females between 60 and 100 days post fertilization. Clustered cDNA sequences were generated and compared to the zebrafish ¿Gonad Uniclone¿ cDNA set to identify novel clones expressed very early during testis formation. When mapped to the zebrafish genome common carp cDNAs identified a number of novel genes, which were not predicted by either experimental or bioinformatic methods.