Glucose-6-phosphate dehydrogenase (G6PD) deficiency is the most common human metabolic disorder in southern China. We investigated the incidence and distribution of mutations, the molecular pathology of affected females and the haplotype association with G6PD deficiency in patients from the Guangxi region.A population-based molecular analysis combining phenotypic screening and genotypic detection using both multiplex primer extension/denaturing high performance liquid chromatography assay and DNA sequence analysis were performed in a total of 4,704 individuals.The mutation frequency of male G6PD-deficient individuals was observed to be 7.43%. Twenty-seven genotypes from 361 individuals were found. Statistical analysis showed that there were significant differences in both the percentages of methemoglobin and the G6PD/6PGD ratio between heterozygote and hemizygote in males and between heterozygote and homozygote in females. However, no statistically significance was seen between hemizyotes and homozygotes. The mutation profile showed that five mutations, G6PD Kaiping(1388A), G6PD Canton(1376T), G6PD Gaohe(95G), Chinese-5(1024T)and G6PD Viangchan(817A), are the most common in the area, accounting for 85% of the G6PD-deficient alleles. Ten rare mutations were detected in approximately 4% of the mutant chromosomes. Four novel mutations were found: G6PD Liuzhou(442A), G6PD Nanning(703T), G6PD Laibin(1414C,) and G6PD Hechi(202A/817A). In addition, two other rare mutations, c.196T-->A and c.202 G-->A, were detected for the first time in Chinese patients. A single dominant haplotype (- - + - -) was observed in 94.0% of 182 deficient chromosomes.Our protocol could be used to extend the knowledge of molecular defects of G6PD gene in different geographical areas.