Infertility devastates the life plans of 8%-12% of couples attempting to conceive for the first time. In about half of these cases a male factor is causative. Interestingly, research in male reproduction over the past 30 years has focused largely on the endocrine control of spermatogenesis and genital tract function, yet only about 1% of male infertility has an endocrine cause; thus, this research has had little effect on the treatment of the infertile male. With advancements in molecular medicine, researchers are now beginning to dissect the genes required for male fertility, although their approaches predominantly take advantage of ever-expanding collections of mouse models. 1 The advent of surgical sperm collection from the epididymis or testis and the development of intracytoplasmic sperm injection (ICSI) have provided the only major technological advances in recent years.While most textbooks state that approximately 30% of male infertility is idiopathic, some experts speculate that perhaps 50% of all male infertility is idiopathic. In part, this speculation reflects our poor understanding of the basic mechanisms that regulate genital tract differentiation and development, spermatogenesis, sperm maturation in the genital tract, and the molecular events required for fertilization and early embryonic development; and, hence, our inability to properly diagnose the cause of the infertility. Indeed, commonly used diagnostic categories for male infertility are descriptive and not usually mechanistically based. Accordingly, our ability to properly diagnose and counsel male factor infertile couples is limited. Nevertheless, research shows that genetic defects in male factor infertility are more common than originally believed. These findings have raised concerns that since the assisted reproductive technologies essentially overcome the natural barriers to defective sperm fertilization, mechanisms may now be bypassed that prevent the transmission of genetic defects to offspring of these genetically infertile men.Recognizing this diagnostic limitation, there are nevertheless important clinical genetic tests that should be used today in the diagnosis of the infertile male. The karyotype remains the gold standard of chromosomal analysis and provides important insights regarding the presence of both numerical and structural chromosome abnormalities. Although chromosomal abnormalities are uncommon in fertile men, routine karyotyping suggests that these abnormalities are present in about 6% of infertile men. 2 Defects include human trisomies that result from aberrant recombination during gametogenesis such as sex chromosome abnormalities, which are among the most common human trisomies. 3 For