The immune system, besides orchestrating the immune response, plays an important role in the regulation of tissue homeostasis. We refer to this later activity as ‘immune physiology.’ In human ovaries, immune system-related cells and molecules accompany corpus luteum development and regression and cancer progression. They also accompany the origination of new rat and human germ cells by asymmetric division of ovarian surface epithelium cells, symmetric division and migration of germ cells, and follicular growth. Currently prevailing dogma on the preservation of human oocytes from the fetal period until menopause (‘storage’ doctrine) vs. oocyte renewal in invertebrates and lower vertebrates (‘continued formation’ doctrine) raises question as to the disadvantage from an evolutionary point of view of prolonged oocyte storage in humans. We attempted to reconcile these two opposing views by proposing the prime reproductive period (PRP) doctrine as follows: The ‘storage’ doctrine fits two periods of the life in human females, that between the termination of fetal oogenesis and puberty or pre-menarcheal period (about 10–12 years), and also that period from the end of PRP (at about 38 years of age) until menopause. On the contrary, the ‘continued formation’ doctrine accounts for oocyte and follicular renewal during the PRP, and insures the availability of fresh oocytes for the development of healthy progeny. Further study on ‘immune physiology’ may help us better understand ovarian physiology and pathology in general, including infertility caused by premature ovarian failure, the pathophysiology of degenerative diseases and mechanisms of malignancy and metastasis.