The human aromatase gene (CYP19A1) has eleven tissue-specific untranslated first exons, while only three have been described in the mouse Cyp19A1 namely brain-, ovary- and testis-specific exons 1. The present study aims to elucidate the complete structure of the mouse Cyp19A1 gene. We detected aromatase transcripts in mouse bone, aorta, hypothalamus, adipose, gonads and placenta, but not nulliparous mammary fat pad. BestFit algorithm analysis against the human CYP19A1 has identified ten putative first exons upstream of mouse Cyp19A1. Based on these putative sequences, we were able to design specific primers for RT-PCR and detected for the first time, the presence of exons I.4 and I.3 in murine fat and gonads, respectively. These are novel 5'UTRs of mouse Cyp19A1. Using RT-PCR and 5' RACE, we confirmed the expression of exon 1f in the hypothalamus and proximal exon P2 in the ovary. The testis-specific exon 1 begins 217bp further upstream than previously reported. Putative exons 2a, I.5, I.7, I.6 and I.2 were not detected in mouse tissues. Therefore, we showed that mouse Cyp19A1 contains more tissue-specific first exons than previously thought and displays a similar genomic organization to human CYP19A1.