Developments in genomic medicine will likely explain much of what is now considered idiopathic male infertility. Indeed, our understanding of the genetic defects that cause infertility is no longer confined to chromosomal aneuploidies (e.g., Klinefelter syndrome) and single-gene defects (cystic fibrosis and congenital absence of the vas deferens). The past decade has seen that isolated Y-chromosomal loci can influence spermatogenesis (AZF regions) and that the human X chromosome is likely to be an important source of spermatogenesis genes. More recently, the finding that faulty recombination occurs in male infertility has large implications not only for the cause of the infertility but also for the use of affected gametes. Indeed, as our understanding of genetic infertility matures, so too will the importance and complexity of genetic counseling and testing for patients who use assisted reproduction.