World wide about 2% of men have a primary deficiency in sperm production. Familial cases of male infertility and chromosomal anomalies associated with this phenotype indicate that there is, at least in some cases, a genetic cause. In particular, deletions of the non-recombining portion of the Y chromosome are associated with a failure of sperm production. Deletion screening, using Y-specific markers has defined three regions (AZFa, b, c) that are associated with azoospermia. Each region contains one or more candidate genes that may be responsible for the phenotype. However, mutations have not yet been identified in any of these genes. This review discusses the structural organisation of the human Y chromosome and genes that are candidates for male infertility.