Male infertility is a common health issue in men with ever increasing incidence. Unfortunately, available diagnostics are inadequate to drive clinical decision making in the vast majority of cases. New forms of diagnostics are needed to provide more personalized care and to improve outcomes. One area of recent interest is the diagnostic utility of sperm epigenetics. While becoming more common to explore, there are still many unknowns regarding the potential of these marks to drive clinical care. We will discuss the unique epigenetic marks in sperm and how these can potentially be used to provide clinically actionable care for some of the most difficult cases of male infertility, namely, cryptozoospermia and azoospermia.