Objective To study the diagnostic significance and clinical value of genetic analysis in children with neonatal diabetes. Methods Gene mutation analysis was performed in four patients from Zhengzhou children ' s hospital with diagnosis of with neonatal diabetes. Therapeutic effect of glibenclamide in patients with or without gene mutation was compared. Results KCNJ11 gene mutation was found in two patients with neonatal diabetes. Glibenclamide was found only effective for blood glucose control in patients with KCNJ11 mutation. Therefore, Insulin remains the best therapeutic choice in patients without the genetic mutation. Conclusions Genetic mutation status may be useful in choosing treatment options of neonatal diabetic patients, therefore, should be performed in all children with neonatal diabetes.