Granulosa cells feed the oocyte during its maturation and protect it. Aberrant apoptosis in these cells is known to ultimately impair oogenesis. The current knowledge of how extragenital inflammation affects apoptosis in granulosa cells is incomprehensive, which is the root of an urgent problem connected to the spread of inflammatory diseases and the growing level of female infertility. This study aimed to assess the intensity of granulosa cell apoptosis in women with impaired reproductive function that suffer from chronic respiratory and/or digestive system diseases of inflammatory origin, and to identify the link, if any, between the studied factor and dysfunction of the reproductive system in the test group. The group included 60 women with a history of respiratory and/or digestive system inflammatory pathology that underwent IVF in 2021–2022. The women were donors of the granulosa cells from the follicular fluid collected through transvaginal puncture of preovulatory follicles. We studied the apoptosis process with the help of flow cytometry. For statistical analysis, we used the Fisher's F-test and the Kruskal–Wallis test. Twenty participants without extragenital pathology in their medical histories, the first subgroup, had the level of apoptosis in granulosa cells at 0.0088 ± 0.0062%, which is significantly lower than in twenty donors with a history of chronic inflammatory digestive system diseases, the second subgroup (granulosa cell apoptosis at 0.0140 ± 0.0099%, p = 0.015), and the subgroup of women suffering from inflammatory diseases of the respiratory system (granulosa cell apoptosis at 0.0650 ± 0.0391%, p = 0.033); the efficacy of IVF was higher in the first subgroup.