The role of estrogen and testosterone in the regulation of gene expression in the proximal reproductive tract is not completely understood. To address this question, mice were treated with testosterone or estradiol, and RNA from the efferent ducts and caput epididymides was processed and hybridized to Affymetrix M430 2.0 microarrays. Analysis of array output identified probe sets in each tissue with altered levels in hormone-treated versus control animals. Hormone treatment efficacy was confirmed by determination of serum hormone levels before and after treatment and by observed changes in transcript levels of previously reported hormone-responsive genes. Tissue-specific hormone sensitivity was observed with 2867 and 3197 probe sets changing significantly in the efferent ducts after estrogen and testosterone treatment, respectively. In the caput epididymidis, 117 and 268 probe sets changed after estrogen and testosterone treatment, respectively, demonstrating a greater response to hormone in the efferent ducts than in the caput epididymidis. Transcripts sharing similar profiles in the intact and hormone-treated animals compared with castrated controls were also identified. Ontology analysis of probe sets revealed that a significant number of hormone-regulated transcripts encode proteins associated with lipid metabolism, transcription, and steroid metabolism in both tissues. Real-time RT-PCR was used to confirm array data and to investigate other potential hormone-responsive regulators of proximal reproductive tract function. The results of this work reveal previously unknown responses to estrogen in the caput epididymidis and to testosterone in the efferent ducts, as well as tissue-specific hormone sensitivity in the proximal reproductive tract.