We have used a simple and efficient method to identify condition-specific transcriptional regulatory sites in vivo to help elucidate the molecular basis of sex-related differences in transcription, which are widespread in mammalian tissues and affect normal physiology, drug response, inflammation, and disease. To systematically uncover transcriptional regulators responsible for these differences, we used DNase hypersensitivity analysis coupled with high-throughput sequencing to produce condition-specific maps of regulatory sites in male and female mouse livers and in livers of male mice feminized by continuous infusion of growth hormone (GH). We identified 71,264 hypersensitive sites, with 1,284 showing robust sex-related differences. Continuous GH infusion suppressed the vast majority of male-specific sites and induced a subset of female-specific sites in male livers. We also identified broad genomic regions (up to ϳ100 kb) showing sex-dependent hypersensitivity and similar patterns of GH responses. We found a strong association of sex-specific sites with sex-specific transcription; however, a majority of sex-specific sites were >100 kb from sex-specific genes. By analyzing sequence motifs within regulatory regions, we identified two known regulators of liver sexual dimorphism and several new candidates for further investigation. This approach can readily be applied to mapping condition-specific regulatory sites in mammalian tissues under a wide variety of physiological conditions. Sexual dimorphism in gene expression is common in mammalian somatic tissues (23) and has broad implications for human health. Sex differences in gene expression may contribute to differences between men and women in the prevalence, extent, and progression of disease, including autoimmune diseases (54), kidney disease (37), cardiovascular disease (45), and liver diseases, such as hepatocellular carcinoma (9, 58). In addition, sex-related differences in pharmacokinetics and pharmacodynamics are common and may affect drug response (52). Sex-related differences in gene expression have been widely studied in liver, where they affect Ͼ1,000 transcripts (5, 51, 57) and impact physiological and pathophysiological functions ranging from lipid and fatty acid metabolism to xenobiotic metabolism and disease susceptibility (52). In the liver, sexrelated differences in gene expression are primarily determined by growth hormone (GH) signaling (3, 21), which shows important sex-related differences that reflect the sex-related differences in plasma GH profiles seen in many species, including rats, mice, and humans (53).The underlying mechanisms of sexual dimorphism in mammalian tissues have been only partly elucidated at the molecular level. In the male rat liver, intermittent plasma GH pulses repeatedly activate the latent cytoplasmic transcription factor STAT5b, whose activity is essential for sex-related differences in the liver (5). The more continuous, female-like pattern of pituitary GH secretion can be mimicked by continuous GH infusion in mal...