Pathogenic variants in MPDZ are typically associated with congenital hydrocephalus. We report on siblings who present with more complex central nervous system malformations and defects in cardiovascular, ocular, and respiratory systems. Phenotyping of the proband revealed aortic coarctation, bicuspid aortic valve, partial anomalous pulmonary venous return, ventricular septal defect, Dandy-Walker malformation, along with subependymal gray matter heterotopia, megalocornea, and chorioretinal punctate lesions. Prenatal phenotyping of the proband's now deceased brother noted left-sided diaphragmatic hernia, a single cardiac ventricle of right ventricular morphology, aortic and mitral valve hypoplasia with aortic coarctation, ventriculomegaly, and mega cisterna magna. Whole genome sequencing identified a homozygous likely pathogenic canonical splice site variant in MPDZ, c.2650-1G>A in both siblings. These siblings present with features suggesting that MPDZ pathogenicity may be associated with a more complex syndromic neurodevelopmental phenotype with both central nervous system and non–central nervous system features. We speculate that MPDZ influences common morphogenetic pathways underlying these relationships.