A total of 1,000 school boys ages 14-18 years, were randomly selected from six schools of Kermanshah and screened for G6PD deficiency. Fifty-three out of 1,000 were found to be severely G6PD deficient giving a frequency of 5.3% for G6PD deficiency in males in Kermanshah. We performed DNA analysis on 68 G6PD deficient children, 52 school boys and 16 children with the history of favism and hemolytic anemia using a combination of PCR-RFLP technique, single strand conformation polymorphism (SSCP) analysis and DNA sequencing. Three polymorphic G6PD mutations were identified: G6PD Mediterranean, Chatham and Cosenza. The commonest allele was found to be the G6PD Mediterranean (91.2%) followed by the G6PD Chatham (7.3%) and the G6PD Cosenza (1.5%). Haplotype analysis revealed that 56 out of 62 (90%) G6PD Mediterranean was linked to haplotype BclI(+) (1311T). In contrast, all G6PD Chatham and Cosenza had haplotype BclI(-) (1311C). The polymorphism IVS11-93 (T-->C) was present in 88.5% of the subjects studied. Only 4/55 (7.3%) of the Mediterranean alleles were associated with the T form and were always related to the nt 1311C. Our findings indicate that the allele frequency of G6PD Mediterranean mutation in Kermanshah is higher than those from two Fars ethnic groups living in Northern and Southern Iran. Nevertheless, they are in strict accordance with a previous report of the prevalence of the G6PD Mediterranean in Kurdish and Middle East population. Also, of strong association of the G6PD Mediterranean mutation and the presence of the polymorphism nt 1311C-->T in the Kermanshah population demonstrate that the presence of this mutation may be the result of migrations that have taken place through the history of Iran.