On the concave surface of the ovary is the ovulation fossa where the oocyte is expelled from the ovary. The outer layer of the ovary is the medulla (contains the blood vessels and nerves). The inner layer, cortex, contains the follicles.

The filly is born with all the oocytes (eggs) in the ovary. The oocytes, in primordial follicles, are surrounded by a single layer of cells. At puberty, some of the oocytes in the primordial follicles and associated follicle cells begin to grow and become primary follicles. As the follicle and oocyte continue to grow, multiple layers of follicle cells form and the follicle is now called a secondary follicle. The follicle continues to grow, a cavity forms, the follicle cells differentiate into several layers, estrogen is produced, and the follicle is now known as a tertiary follicle. The tertiary follicle can grow very large, 45 - 55 mm (1.5 to 2 in.) before it will rupture to release the oocyte at ovulation. The follicle that will eventually ovulate is known as the dominant follicle and moves toward the ovulation fossa as it approaches maximum size. Importantly, many follicles can start development but most die through a process known as atresia. Only 1 or 2 follicles will ovulate every 21 days during the breeding season. Any follicles developing during the non-breeding season will become atretic before completing development.

After ovulation, the cells that remain in the follicle divide and begin to produce progesterone. The ovulated follicle forms the corpus luteum (CL). The CL produces progesterone for 14-15 days. If the mare is not pregnant, the CL regresses and stops producing progesterone. The structure becomes a corpus albicans and will become less organized and disappear. The hormonal control of the cycle will be discussed in another lecture.