This study has two aims: [1] to evaluate the association between hOGG1 genotypic polymorphism and endometriosis risk, and [2] to investigate the joint effects of hOGG1 genotype and smoking habit on endometriosis susceptibility in Taiwan. For this purpose, the well-known polymorphic variants of hOGG1, codon 326, was genotyped and analyzed of its association with the risk of endometriosis. In total, 153 patients with endometriosis and 636 non-endometriosis healthy controls were recruited and genotyped. The methodology for genotyping is polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP). Pearson's Chi-square test was performed to compare the distributions of the genotypes between case and control groups. The results showed that the hOGG1 codon 326 genotypes were not differently distributed between the endometriosis and non-endometriosis control groups in both genotypic (P = 0.6212) and allelic (P = 0.4006) frequency analysis. We have further analyzed the genotypic-smoking joint effects on endometriosis risk and found an obvious interaction between hOGG1 codon 326 genotypes and smoking status. The hOGG1 codon 326 genotypes were increased in endometriosis risk only in the smoker groups (P = 0.0061), but not in the non-chewer group (P = 0.0648). Our results provide the evidence that the hOGG1 codon 326 genotype may have a joint effect with smoking on the development of endometriosis.