The molecular and biochemical mechanisms contributing to the development and progression of both prostate and ovarian carcinogenesis are currently unknown. A better understanding of the cross-talk between endocrine, signal transduction and regulatory pathways in normal and neoplastic prostatic and ovarian tissues is necessary to elucidate malignant progression in these tissues. This review compares these two malignancies with reference to androgens and the androgen receptor. In particular, the expression and relevance of androgen-regulated genes are discussed. Cytokines, co-activators and co-regulators that interact or effect the androgen receptor are also considered. With increased understanding of the molecular mechanisms of prostate and ovarian carcinogenesis, the identification and development of novel and existing biomarkers may become more achievable.