Apoptosis is a type of physiologic cell death that occurs in many tissues and may be regulated by peptide growth factors. Recent studies indicate that apoptosis occurs in the ovary during follicular atresia in several animal species, including the rat, pig, chicken, baboon, and rabbit. The purpose of this study was to demonstrate, through in situ identification of apoptotic cells in intact ovarian sections, the sites in which apoptosis occurs in the rat ovary in different functional states. We evaluated the presence of apoptosis in three models: immature rats, eCG-treated rats and adult cycling rats. Paraffin ovarian sections were pretreated with proteinase K and then end-labeled with biotinylated deoxyuridine triphosphate (dUTP) by incubation with the enzyme terminal deoxynucleotidyl transferase (TDT). They were then stained through use of avidin-conjugated peroxidase with 3,3′-diaminobenzidine as the substrate. Healthy antral and preantral follicles had no staining. The nuclei of granulosa cells of preantral and antral atretic follicles were positively stained in all the animal groups. Scattered theca cells were also stained. Stromal cells were consistently negative. Positive controls were sections pretreated with DNase I; these displayed intense staining of all nuclei. Negative controls, in which either terminal TDT or its biotinylated substrate was omitted, were appropriately negative. This study represents a systematic analysis of apoptosis in the rat ovary at different functional stages and supports the hypothesis that apoptosis is involved in the process of follicular atresia.