There is a lack of appropriate classification criteria for the determination of atretic follicles in guinea pigs. In the present study, new criteria were established based on the latest morphologic criteria for cell death proposed by the Nomenclature Committee on Cell Death (NCCD) in 2009. Ovaries of guinea pigs were sampled on different stages of estrous cycle, and the morphologic observations of atretic follicles were investigated in serial sections. The results showed that the process of follicular atresia could be classified into four continuous stages: (1) the granulosa layer became loose, and some apoptotic bodies began to appear; (2) the granulosa cells were massively eliminated; (3) the theca interna cells differentiated; and (4) the residual follicular cells degenerated. In addition, the examination revealed that these morphologic criteria were accurate and feasible. In conclusion, this study provides new criteria for the classification of atretic follicles in guinea pigs, and this knowledge can inform future research in the area.