The authors present an exceptionally rare case of a newborn in whom total anomalous pulmonary venous return (TAPVR) had been diagnosed prenatally and in whom genetic testing after neonatal cardiac repair confirmed a missense variant of the FBN1 gene consistent with Marfan syndrome as well as a PRKDC gene mutation associated with severe combined immunodeficiency. To the authors' knowledge, this is the first reported case with this unique combination. Neonatal TAPVR repair was undertaken with a good postoperative outcome and survival until the last follow-up.