According to the latest data, globally 15% of couples have infertility and male infertility contributes to 10% of all cases. Infertility can be caused by certain biological changes in the gonads and the reproductive system like azoospermia, oligospermia, asthenospermia, teratozoospermia and hypospermatogenesis. Genetic causes of azoospermia include chromosomal abnormalities, Y chromosome microdeletions and deletion or other mutations of Y-linked genes. The maximum number of the genes are located in the azoospermia factor region of the long arm (Yq) of the Y chromosome. Y chromosome microdeletion is known as the second major genetic cause of spermatogenetic failure. This article aims to review the latest updates on the involvement of Yq microdeletions in male infertility. The diagnostics, prevalence and phenotypic spectrum related to Yq gene microdeletions are discussed.