In the perinatal ovary of most mammals, external and internal factors establish a primordial follicle reserve that specifies the duration of the reproductive lifespan of a given species. We analyzed the mechanism of follicle loss and survival in C57BI/6 mice using static and dynamic assays of apoptosis, autophagy, and ovarian morphogenesis. We confirm an initial loss soon after birth, when about 44% of the germ cells detectable at the end of the fetal period abruptly disappear. The observations that (1) few germ or somatic cells were apoptotic in newborn ovaries, (2) vitally stained organ cultures exhibit active extrusion of non-apoptotic germ cells and (3) germ-cell lysosome amplification occurs at birth suggested that additional mechanisms are involved in perinatal germ cell loss. Newborn mouse ovaries cultured in the pH sensitive dye lysotracker red exhibit an increased incidence of acidified non-apoptotic germ cells when maintained in the absence but not in the presence of serum, implying a role for autophagy in germ cell attrition. Inhibitors of autophagy, but not apoptosis, reduce germ cell acidification induced by serum starvation in ovary organ cultures and protein mediators of both autophagy and apoptosis are expressed at birth. From these findings we suggest that multiple perinatal mechanisms establish the primordial follicle reserve in mice.