© 2022 The Author(s).Topical steroids (TS) have been widely prescribed since the 1950s. This study investigated for the first time the transgenerational effects of TS on the antioxidant mechanism of the hypothalamus-pituitary-adrenal (HPA) axis, both in prenatal and infancy. Three generations (F1, F2, and F3) and prenatal group (P) were investigated in both sexes with two different time points; P45th and P75th day were accepted as puberty and early adulthood, respectively. Clobetasol propionate 0.05% was used as TS. Quantitative real-time PCR was performed to expressional analyses of Sod1, Sod2, and Sod3 genes in the HPA tissues. The Sod mRNA expression of the HPA belonging to P and F1 groups revealed similar results in both genders. The downregulation in the adrenal Sod level was determined in P and F1, F2, and F3 generations in both genders, especially in females (p < 0.05). The Sod activities in the pituitary of all groups were downregulated in female rats (p < 0.05). Interestingly, in male rats, Sod2 and Sod3 were not expressed in the pituitary compared with the control on the day P45, while Sod2 and Sod3 expressions were determined in all the groups on day P75. Sod1 overexpression was found in pituitary and hypothalamus of males in the F3 generation. This study showed that TS applied in infancy had a transgenerational adverse effect on antioxidant defense mechanisms, especially in the adrenal gland.