Comparing female and male brain structures reveals a variety of sex differences in many vertebrates. Some of these differences are thought to be induced during the fetal period by the effect of steroid hormones produced in the gonads. Not much is known about molecular mechanisms involved in gender-specific development of the brain. We have taken a broad approach to isolate sex-specific genes from 18.5 days post coitum brain (A. Eriksson, C. Wahlestedt and K. Nordqvist. 1999. Isolation of sex-specific cDNAs from fetal mouse brain using mRNA differential display and representational difference analysis. Mol. Brain Res., 74, 91-97). Female and male mouse brains were screened with the signal peptide differential display, developed in our laboratory, and with a modified representational difference analysis of cDNA. The resulting sex-specific fragments were verified by semi-quantitative RT-PCR. Here we describe these methods in detail.