This case report describes the neuropathological findings in an autopsy case of short rib-polydactyly syndrome (SRPS). The patient was a Japanese female neonate who was born at 35 weeks of gestation and died soon after birth due to severe cardiopulmonary insufficiency. Clinical and radiological findings were most consistent with SRPS type I (Saldino-Noonan type). General autopsy findings included situs inversus, persistent truncus arteriosus and endocardial cushion defect, hypoplastic lungs and adrenal glands, and vaginal atresia. Fixed brain weight was 330 g. Three different categories of pathological changes were detected in the brain. These were as follows: (1) multiple cyst formation in the parenchyma, (2) primary malformations of the nervous and mesenchymal tissues, and (3) deposition of an unusual substance in the cerebral white matter. The multiple cysts or cavities in the parenchyma may be due to severe hypoxic-ischemic insults related to the congenital heart anomaly. The primary malformations were summarized as follows: (1) capillary telangiectasia of the pia mater and choroid plexus, (2) olfactory dysplasia with asymmetry, (3) focal cortical dysplasia in the frontal lobe and cerebellum, (4) olivary dysplasia, and (5) enlargement of the posterior part of the lateral ventricle. Dysplastic changes of the nervous tissue can be classified into the group of neuronal migration disorders. Although biochemical properties of the unknown substance were not determined, it is considered to be some product derived from an inborn error of metabolism. Morphological data of SRPS is still scarce, and pathognomonic changes have not yet been elucidated. The present data suggests that coexistence of the nervous and mesenchymal malformations may be highly characteristic of SRPS.