Azoospermia is caused by abnormality in the various genes involved in spermatogenesis. However, the crucial genes for spermatogenesis have not yet been identified. Recently, targeted knockout and transgenic mice have been generated and considerable knowledge has been accumulated about their phenotype patterns, and a wide variety of genes are known to be associated with sperm formation. First, we review the meiotic and post-meiotic phases and genes expressed during spermatogenesis. Many genes corresponding to various clinical features of azoospermia exist, and we also review azoospermia related genes from clinical aspects. The AZF (azoospermia factor) regions on the Y chromosome long arm are thought to show a major correlation with spermatogenesis. From the genomic point of view, their deletion due to intrachromosomal recombimation is reviewed as a constitutional feature of the Y chromosome. Moreover, we explain how to use a detection kit for the Y chromosome micro deletion which we developed.