Idiopathic male infertility is often associated with genetic and epigenetic abnormalities. Such abnormalities include chromosome translocations and aneuploidies, Y chromosome microdeletions, and mutations of the CFTR gene. The unraveling of the human genome and ongoing animal transgenic studies have identified numerous other genes likely to be associated with male infertility. Initial reports from human studies have identified several candidate genes, including the protamine genes, SPO11, EIF5A2, USP26, ACT, and others. In addition to gene mutations and polymorphisms, damage to the chromatin resulting in single and double strand DNA breaks affects fertility. Recent studies are highlighting the role of such abnormalities in male infertility, and point to protamine defects as one cause of DNA damage. Epigenetic abnormalities also are being investigated, including the role of residual sperm mRNA in embryogenesis, and the effects of abnormal spermatogenesis on gene imprinting. These studies are pointing to complex etiologies and clinical ramifications in many infertile men.