Cryptorchidism is the most common congenital disorder in boys; one major complication of this disorder is male infertility. Androgens are key hormones to complete testicular descent; therefore, impaired fetal androgen action can result in this anomaly; its molecular etiology, however, remains unknown. Recent molecular approaches might provide an opportunity to identify not only candidate genes but also several predictive markers of future fertility. The purpose of this review is to summarize the recent insight into the genetic pathway of testicular descent and the molecular etiology of isolated cryptorchidism, and discuss the prospects of treatment to achieve future fertility in such patients.