Objectives To determine the prevalence of glucose-6-phosphate dehydrogenase (G6PD) deficiency in Isfahan, the central state of Iran. Methods From February to March 2006, a total of 2501 samples were screened for the quantitative measurement of G6PD activity by enzymatic colorimetric assay by a commercial kit (GAMMA, Belgium). The neonates were referred from 17 delivery units to the Isfahan neonatal screening center at 3–7 days after birth. Any neonate with a value < 6.4 U/gHb was considered G6PD deficient. Results Of the 2501 newborns (1307 males, 1194 females) screened, 79 neonates were found to have G6PD deficiency (67 males, 12 females). The overall incidence of G6PD deficiency was 3.2%. Frequency in male population was 5.1 % (67 out of 1307 male neonates) and in female population was 1% (12 out of 1194 female neonates).The female:male ratio was 1:5.5 ( P = 0.0001). The mean enzyme activity in deficient patients was 3.22 ± 1.8 U/gHb (male deficient group; 3.17 ± 1.74 U/gHb, female deficient group; 3.49 ± 2.17 U/gHb, P = 0.58). Conclusion Routine neonatal screening in Isfahan, Iran with a relatively high prevalence of G6PD deficiency is justified and meets the World Health Organization recommendation.