Follicular atresia is a key event in the selection of the ovulatory follicles and occurs during all developmental stages. The aims of the study were to evaluate the follicular population as well as the rates of follicular recruitment and atresia in different strains of mice. Ovaries were obtained from four strains of mice: G1/Swiss, G2/F1 Swiss×C57BL/6, G3/inbred strain C57BL/6, and G4/F1 C57BL/6×Swiss. All mice used in the study were 60 days old. Ovaries collected from the mice were fixed and processed for histological analysis. The G2 ovaries were also used to examine immunolocalization of active caspase-3. The pimordial follicle population was smaller in G3 mice than in G1, G2 and G4 groups (7 565±1 845 vs. 17 180±3 159, 14 785±3 319 and 13 325±2 685, respectively; p<0.05). The rate of follicular recruitment in G3, however, was higher than in the other groups (29.2% vs. 18.2%, 17.3% and 13.0% in G1, G2 and G4, respectively; p<0.05), resulting in a similar (p>0.05) number of antral follicles among groups. The small follicular pool in G3 mice was also associated with a lower rate of follicular atresia (11.4% vs. 17.2%, 16.7% and 13.6% for G3, G1, G2 and G4, respectively; p<0.05). The number of follicles stained with active caspase-3 was higher (p<0.05) during the final stage of preantral folliculogenesis than in other stages of follicular development suggesting that apoptosis in mice occurs earlier in comparison to large animals. Thus, it was concluded that differences in follicle reservoir among mice strains are compensated by an increased rate of follicular recruitment and a decreased rate of follicular atresia; and atresia occurs in mice mainly at the end of the preantral stage of folliculogenesis.