We describe the application of optical coherence tomography (OCT) for noninvasive analysis of follicular development in mouse ovaries. Ovaries contain many follicles and oocytes. Quantification of follicles at various developmental stages is an indication of the ability of an ovary to provide oocytes capable of fertilization. Three-dimensional structural OCT images identified each developmental stage, from a primary follicle (50 μm in diameter) to an antral follicle (350 μm in diameter), in the ovary of a 25.5-day-old mouse. We discovered time-varying OCT signals at the oocytes that differentiated them from surrounding tissues. These signals were clearly enhanced by interframe intensity-based Doppler OCT techniques. The OCT technology was effective in analyzing the development of follicles and oocytes in ovaries.