The long arm of the human Y chromosome is required for male fertility. Deletions in three different regions can cause severe spermatogenic defects ranging from non-obstructive azoospermia to oligozoospermia. Use of intracytoplasmic sperm injection (ICSI) may allow Y chromosome defects to be passed from father to son. Thus, numerous reports have stressed the need to offer genetic testing to infertile men who select ICSI and a number of reproductive clinics have begun to do so. The primary objectives of this review were: firstly, to discuss the characteristics of the published set of polymerase chain reaction markers and how these characteristics affect interpretation of Y chromosome deletion analysis and secondly, to summarize the recent literature pertaining to the genes on the Y chromosome.