Genome sequencing data have been accumulating exponentially. The detection and analysis of a tremendous amount of genetic information require new rapid, highly-efficient techniques of hybridization and sequencing. The development of high-through genechip technology has dramatically enhanced our ability in male infertility research. Current applications of genechip technology in male infertility include the study of testis genes, the analysis of spermatozoon mRNA, the study on cell genital toxicity, the diagnosis and treatment of male infertility. This review summarizes the present situation in male infertility research and the potential clinical application.