Male infertility is a common complex disease. Y-linked spermatogenic failure is an important cause for this disorder. Due to the presence of many repeat sequences and the frequent occurrence of non-allelic homologous recombination between the sequences in the male-specific region of the Y (MSY) region of the chromosome, Y chromosome possesses high variation rate. The variations may result in the dosage changes of spermatogenesis-related gene families and lead to male infertility. The present article reviews the recent progress of the study on Y chromosome variations, and its possible effect on spermatogenic function, in DNA level.