Background Methylation defects at chromosome 6q24 usually induce transient neonatal diabetes mellitus. There are few reports of permanent neonatal diabetes mellitus caused by abnormalities of 6q24. We report the first case of permanent neonatal diabetes mellitus to be associated with confirmed methylation defects at chromosome 6q24. Case report A baby girl, small for her gestational age, was found to have high blood glucose 1 day after birth, with no systematic congenital anomalies. She showed no remission of diabetes and has hitherto been reliant on insulin (now aged of 5.5 years), which supports a diagnosis of permanent neonatal diabetes mellitus. The single nucleotide polymorphism array and highly polymorphic short tandem repeat analysis identified paternal uniparental disomy of chromosome 6, and a genome-wide analysis ruled out mutations in coding and non-coding regions. Conclusion This report expands the varieties of neonatal diabetes known to be induced by methylation defects at chromosome 6q24, and suggests that the diagnostic evaluation of permanent neonatal diabetes mellitus should be expanded to include testing for 6q24.