Isotretinoin use as a treatment for acne has increased tremendously and, with it, the problems of associated birth defects. We feel that pathologists should be familiar with isotretinoin embryopathy and its pathogenesis in order to assist in differentiating this syndrome from other genetic syndromes that involve branchial arch defects, such as DiGeorge syndrome or velocardiofacial syndrome. Although selected autopsy findings have been presented in epidemiologic reports, to our knowledge a detailed autopsy report has not been published. We therefore wish to present a complete case study of isotretinoin embryopathy that illustrates the pathologic diagnostic criteria and correlates these with the clinical findings. Although the syndrome's major features are explained by the drug's effect on neural crest cells, it has been postulated that isotretinoin also affects other cells in the central nervous system. Our current case supports this theory and shows that these changes in the nervous system may present significant functional impairment, while not presenting visible anatomic changes on either imaging studies or routine histologic examinations.