In many countries screening for Glucose-6-Phosphate Dehydrogenase (G6PD) is a part of the newborn screening program. In Indonesia the National Newborn screening program started in 2012 exclusively for Congenital Hypothyroidism and screening for G6PD has not been included in the National Screening Program. Deficiency of G6PD can cause many manifestations with a high morbidity rate. Different areas in Indonesia might have different proportions of G6PD deficiency. To estimate the prevalence of G6PD deficiencies in Indonesian newborns, Dried blood spot (DBS) samples were collected from many provinces all over Indonesia and were analyzed for G6PD deficiency using Labsystems Neonatal G6PD kit. The study found that the G6PD deficiency was observed in 7.39 male and 6.95% female babies. The cutoff value for G6PD deficiency was less than 4,5 IU/gHb. The proportion was higher in male babies compared to females. Based on this finding, the G6PD screening should be performed in all newborns because the total prevalence was more than 3–5% as stated by the WHO recommendation