RUNX1T1 (ETO) encodes a transcription regulator for hematopoietic genes and is well-known for its involvement in hematologic malignancies, particularly acute myeloid leukemia (AML). However, its role in congenital disease is less understood. This study provides detailed clinical and molecular information on three cases exhibiting neurodevelopmental and congenital anomalies with germline de novo alterations in RUNX1T1. One case features a de novo nonsense variant in the 5' region of the gene (p.Gln36Ter), while the other two harbor de novo missense variants in the C-terminus end (p.Gly412Arg and p.His521Tyr). Common features across cases include craniofacial dysmorphism and neurodevelopmental issues including developmental delay, learning disabilities, attention deficit hyperactivity disorder, and autism. This study, in conjunction with previously reported germline disruptions of RUNX1T1, provides evidence supporting the role of germline RUNX1T1 variation in human congenital neurodevelopmental disorders.