Phylogenetic footprinting was used to predict functional transcription factor binding sites (TFBS) for STAT5, a GH-activated transcription factor, in the GH-responsive genes IGF1, SOCS2 and HNF6. Each gene, including upstream (100kb) and downstream regions (25kb), was aligned across four species and searched for conserved STAT5-binding sites using TFBS matrices. Predicted sites were classified as paired or single, and whether or not they matched the STAT5 consensus sequence TTCN₃GAA. Fifty-seven of the predicted genomic regions were assayed by chromatin immunoprecipitation from male rat liver with high STAT5 activity. STAT5 binding was enriched (up to 24-fold) at eight genomic regions of IGF1, including three novel regions in the second intron, and at four regions of SOCS2, including three novel upstream sites. STAT5 binding to HNF6 was modestly enriched (up to 3-fold) at one consensus site and two novel, non-consensus sites. Overall, 14 of 17 identified sites were paired STAT5 sites. STAT5 binding to these sites was dynamic in male rat liver, cycling on and off in response to each plasma GH pulse. Moreover, sex-specific STAT5 binding was apparent: in female liver, where nuclear STAT5 activity is generally low, STAT5 binding to IGF1 and SOCS2 was limited to high affinity sites. Analysis of the verified STAT5 binding sites indicated that STAT5 TFBS matrix 459 in combination with a STAT5 consensus sequence was the best predictor of STAT5 binding to these three genes. Using these criteria, multiple novel STAT5 binding sites were identified and then verified in several other GH-inducible genes, including MUP genes, where male-specific gene expression was associated with male-specific STAT5 binding to multiple low-affinity STAT5 sites.