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Our observations of bovine follicles indicated that the original histological classifications of atresia were inaccurate. A detailed histological, ultrastructural and immunohistochemical study of antral follicles from bovine ovaries collected from an abattoir and from animals whose large follicles had been monitored by ultrasonography was conducted to investigate this further. Nidogen and CD68 were immunolocalized to observe the follicular basal lamina and macrophages, respectively. In randomly collected ovaries, approximately one quarter of all antral follicles were undergoing antral atresia, as designated in this study. Antral atresia was characterized by early destruction of the layers of the membrana granulosa closest to the antrum, whereas the most basal cells remained intact. Numerous pyknotic nuclei were observed in the most antral layers and in the antrum close to the membrana granulosa. This is the classic description of atretic follicles and was observed at all sizes of follicle development and almost universally in large follicles (> 5 mm in diameter), including dominant follicles. Basal atretic follicles, as designated in this study, were almost as prevalent as the antral atretic follicles, and were characterized by initial destruction of the most basal layer of granulosa cells, whereas the cells in the most antral layers remained associated with each other and were predominantly healthy. Pyknotic nuclei and the nuclei of dying basal cells budded into apoptotic bodies were observed rarely. The basal lamina of basal atretic follicles was often breached by macrophages, which were phagocytosing dying basal granulosa cells. The theca was characterized by an increased deposition of collagen, and the cells were orientated randomly, rather than lying parallel to the membrana granulosa as in healthy follicles. Basal atresia occurred in small (< 5 mm in diameter) follicles only. Importantly, these basal atretic follicles were originally identified incorrectly in the literature. Thus, on the basis of the results of this study and another on the expression of steroidogenic enzymes in atretic follicles, it is suggested that the standard biochemical methods for measuring steroid hormone concentrations in follicular fluids to assess atresia should be re-evaluated.