Permanent neonatal diabetes may occur either in isolation or associated with multi-organ syndromes. It is caused by mutations in the genes responsible for pancreatic β cell mass or function. We report new cases of consanguineous parents from Saudi Arabia with a homozygous deletion of exons 1and 2, and exon 5-9 of the GLIS3 gene, who presented with permanent neonatal diabetes associated with intrauterine growth retardation, severe congenital hypothyroidism without other manifestation in the liver, renal or eyes in the 1^st one and cystic renal changes in the 2^nd patient. Mutations in the GLI-similar 3 (GLIS3) gene encoding the transcription factor GLIS3 are a rare cause of neonatal diabetes and congenital hypothyroidism with only 15 reported patients worldwide to date.