The hypothalamic-pituitary-gonadal (HPG) axis exerts a profound effect on animal development, reproduction, and response to stress, and new insights into its complicated functional activities are continuously being made. In the present study, by using immunohistochemical studies and different mouse models (ovariectomy and ob/ob mice), we systemically analyzed the expression of a novel mitochondria-localized glutamic acid-rich protein (MGARP)/ovary-specific acid protein and demonstrated that MGARP is under the regulation of the HPG axis. MGARP is highly enriched in steroidogenic tissues and the visual system. Interestingly, its expression increases as mice develop. Early in development, MGARP is mainly detected in the retina and adrenal gland. At this early developmental stage, its expression is not detectable in the gonads, but its expression in the gonads dramatically increases during the first 2-4 wk after birth. Importantly, MGARP levels correlate with estrogen levels in the ovaries during the estrous cycle, and estrogen regulates the expression of MGARP in a tissue-specific manner and through a feedback regulatory mechanism. Functional inhibition of GnRH with an antagonist strongly reduces MGARP levels, and knockout of leptin (ob/ob) significantly reduces the MGARP expression in follicular granular cells. We proposed a model that elucidates the role MGARP plays in the HPG axis. Within the HPG axis loop, MGARP participates in hormone biosynthesis while being under the regulation of the hormones derived from the HPG axis.