Abstract: Background and Objective: Isotretinoin cytotoxicity showed to produce more than 35% of congenital defects during pregnancy. Thus, the aim of this study was to evaluate cellular and congenital malformations induced by isotretinoin treatments of female mice during pregnancy. Materials and Methods: A total of 30 female pregnant albino mice were recruited in this study. The animals were classified into 2 groups; the control group (n = 15) and isotretinoin treated group (n = 15). In all groups, pregnant mothers were injected intraperitoneally either with isotretinoin (1 mg kg–1) or with olive oil (0.5 mL) during the stage of organ formation on day 10 of pregnancy. After 20 days of pregnancy, morphometric, morphological, biochemical and histological techniques were evaluated to estimate abnormalities in uterus, ovary, cellular damages in the liver and the kidney of pregnant mothers and their new offspring’s. Results: In this study, isotretinoin at a dose of 1 mg kg–1 b.wt., significantly produced severe cytotoxicity on liver and kidney tissues of pregnant mothers and their new progeny and significantly performed congenital malformations in the development of offspring. Histological, cellular and biochemical examinations signified that isotretinoin cytotoxicity proceeds via cellular apoptotic mechanisms. In mice group treated with isotretinoin, significant fibrosis, apoptosis and both liver and kidney dysfunction were reported in pregnant mothers and their new progeny. Conclusion: The significant liver and kidney dysfunction with congenital malformations in the development of the new offspring's were reported in pregnant mice treated with isotretinoin at a dose of 1 mg kg–1 b.wt. The data signified that isotretinoin cytotoxicity proceeds via cellular apoptotic mechanisms.