An estimated 12% of couples worldwide are infertile. The contributing factor is approximately equal between men and women with nearly 25% diagnosed as idiopathic. Despite the increasing numbers of couples seeking assistance from infertility clinics, few molecular mechanisms have been identified for treatment. Autophagy is an evolutionarily conserved cellular process for bulk degradation and recycling of cytosolic components through the lysosome to maintain homeostasis. Several studies have observed increased levels of autophagy during ovarian folliculogenesis and gonadal steroidogenesis; however, no genetic studies to determine the significance of autophagy exist. To investigate the function of autophagy in the ovary and testis, a directed genetic knockout approach was used to independently knockout two key autophagy genes, Becn1 and Atg7. Chapter 2 reports that deficiency of Becn1 results in 56% fewer primordial follicles at postnatal day 1. In addition, Atg7 knockout mice do not have identifiable primordial follicles, suggesting that autophagy is necessary for survival of female germ cells during embryogenesis. Chapter 3 presents that Becn1 is necessary to sustain pregnancy and the deficiency of Becn1 in granulosa cells is a novel genetic model to study preterm labor due to impaired corpora lutea function. The results indicate that Becn1 is necessary for lipid droplet formation and subsequent progesterone production in luteal cells. In contrast, Atg7 is not necessary and deficiency results in overproduction of progesterone throughout pregnancy, suggesting that the defect in Becn1 conditional knockout mice is additional to autophagy. Chapter 4 presents that Sertoli cell expression of Becn1 is required for spermatogenesis after 8 weeks of age. Beyond 9-weeks-old, Becn1 conditional knockout mice are unable to sire a litter due to a failure of spermatogenesis and a Sertoli-cell-only phenotype in a majority of the seminiferous tubules. Atg7 was also identified as a necessary factor for spermatogenesis beyond 26-weeks-old. Together the data presented in Chapter 4 suggests that autophagy is necessary for adult Sertoli cell function. Primarily, this dissertation presents data from the first functional studies on autophagy in the reproductive tract. The results demonstrate an understanding of the functional significance for Becn1 and Atg7 in both the ovary and testis.