The objective of this study was to determine apoptotic cell localization in preantral and antral follicles of porcine ovaries. Additionally, the proportion of cells undergoing apoptosis was also compared between delayed puberty gilts and normal cyclic gilts. Ovarian tissues were obtained from 34 culled gilts with age and weight of 270.1 ± 3.9 days and 143.8 ± 2.4 kg, respectively. The gilts were classified according to their ovarian appearance as ‘non-cyclic’ (n = 7) and ‘cyclic’ (n = 27) gilts. The terminal deoxynucleotidyl transferase-mediated dUTP nick end labelling (TUNEL) assay was used to determine apoptotic cell expression in different compartments of the ovarian tissue sections. All apparent preantral (n = 110) and antral (n = 262) follicles were evaluated using image analysis software. It was found that apoptotic cells were expressed in both granulosa (22.2%) and theca cell layers (21.3%) of the follicles in the porcine ovaries. The proportion of apoptotic cells in the granulosa layer in the follicles was positively correlated with that in the theca layer (r = 0.90, p < 0.001). Apoptosis did not differ significantly between preantral and antral follicles in either granulosa (27.8% and 26.4%, p > 0.05) or theca cell layers (28.6% and 26.5%, p > 0.05). The proportion of apoptotic cells in non-cyclic gilts was higher than cyclic gilts in both granulosa (31.7% and 22.6%, p < 0.001) and theca cell layers (34.8% and 20.2%, p < 0.001). This study indicated that apoptosis of the granulosa and theca cell layers in the follicles was more pronounced in the ovarian tissue of delayed puberty gilts than cyclic gilts. This implied that apoptosis could be used as a biologic marker for follicular development/function and also that apoptosis was significantly associated with anoestrus or delayed puberty in gilts, commonly observed in tropical climates.