Introduction: Iran is among countries that report a higher prevalence of glucose-6-phosphate dehydrogenase (G6PD) deficiency, ranging from 2.28% to 30.80%. This study aimed to estimate the general prevalence of G6PD deficiency in newborns with jaundice who were hospitalised in southeast Iran. Methods: This was a prospective study. A total of 100 newborns (boys and girls) with hyperbilirubinaemia, presented to Amir Al-Mo’menin Hospital in 2006 and 2007, were selected for the study. Age, gender, weight, time of jaundice, the maximum level of direct bilirubin, and the total level of bilirubin among the newborns were recorded, and the data were analysed by SPSS. Results: A total of 100 jaundice neonates, including 46 girls and 54 boys, were enrolled. Twenty-two percent of these patients, including 18 (82%) boys and 4 (18%) girls, showed low levels of G6PD. The overall mean bilirubin level was 15.45 ± 3.43 mg/dL among neonates with low G6PD levels, while it was 19.21 ± 3.34 mg/dL in patients with normal G6PD levels, which showed a significant difference (p < 0.05). Conclusion: The prevalence of G6PD deficiency in neonates with jaundice in our study was 22%, which was higher compared to other regions. We propose G6PD deficiency screening for the prevention of its complications. We also suggest assessing calcium levels following phototherapy, given the higher prevalence of hypocalcaemia.