Glycine is a simple amino acid that is vital to the proper functioning of the body, but its roles during ontogeny are not well understood. Glycine levels are precisely regulated through the glycine cleavage system (GCS), a complex molecular machine that produces one-carbon units for later metabolism and folate production. Elevated glycine levels due to congenital mutations in GCS components, such as glycine dehydrogenase (gldc), cause devastating human birth defects and the rare disease nonketotic hyperglycinemia (NKH). The exact pathological implications of glycine accumulation are unknown, but NKH patients suffer from pleiotropic symptoms including seizures, apnea, lethargy, severe mental retardation, and early death. Animal models utilizing mice and zebrafish have shown increased ventriculomegaly and motor dysfunction in gldc deficient animals, but have not analyzed organogenesis. Here, we have utilized zebrafish as a genetic platform to explore the roles of gldc during early development. Whole mount in situ hybridization revealed that gldc transcripts were highly expressed in multiple tissues, including the central nervous system and embryonic kidney, recapitulating both mouse and human expression studies. gldc deficiency caused hydrocephalus and pericardial edema, suggesting defects in brain and renal ontogeny. Elevated apoptosis was detected in locations within the brain, kidney, and cloaca. Furthermore, formation of nephron cell populations in the kidney was disrupted in gldc deficient embryos, where the proximal straight tubule was increased at the expense of the distal tubule. Morphological and expression studies revealed severe alterations in brain patterning and morphogenesis as well. Taken together, these studies indicate that gldc has essential roles during early development and have revealed novel functions for pattern formation and cell survival in tissues such as the brain and kidney. Our evidence further emphasizes the zebrafish as a faithful model to examine NKH. Ongoing work with the zebrafish model is poised to expand our medical understanding about the developmental defects consequent to NKH and can be used to perform chemical screens to identify potential therapeutic interventions.