There is often inherent conflict in the overlapping fields of male fertility and andrology. While the goal of all male fertility specialists is to facilitate and preserve biologic paternity, many practitioners also care for a significant number of patients suffering from hypogonadism. Exogenous testosterone administration, the gold standard for the management of these patients, almost universally impairs spermatogenesis and can even completely eradicate it in some men. With steady increases in both the incidence of hypogonadism and average paternal age, practitioners are now encountering hypogonadal men who desire future fertility or men suffering the effects of earlier androgenic anabolic steroid use with increasing frequency. In this manuscript, we review management strategies for these complex patients and explore novel medications that may be of use in this population.