We conducted a molecular epidemiologic study in rural China to investigate the association of the cytochrome P450 2D6 (CYP2D6) and glutathione S-transferase Mu (GSTM1) polymorphisms with dysmenorrhea. This report includes 435 subjects, 129 with and 306 without any history of dysmenorrhea, who did not smoke or drink alcohol. We obtained information on dysmenorrhea and major covariates by questionnaire interview. We used categorical methods and logistic regression models to evaluate the individual and combined associations of CYP2D6 and GSTM1 polymorphisms with dysmenorrhea and its subgroups, occasional (N = 70) and recurrent (N = 59), with adjustment for age, education, occupation, passive smoke exposure, age of menarche, parity, contraceptive method, height, and body mass index. Both variant CYP2D6 and GSTM1 genotypes were associated with increased risk of recurrent dysmenorrhea [for CYP2D6, odds ratio (OR) = 1.7 and 95% confidence interval (95% CI) = 0.9-3.1; for GSTM1, OR = 1.8 and 95% CI = 1.0-3.4). There was no appreciable association between these variant genotypes and occasional dysmenorrhea. When both the CYP2D6 and GSTM1 genotypes were considered together, the highest risk of recurrent dysmenorrhea was found among women with variant genotypes in both CYP2D6 and GSTM1 (OR = 3.1; 95% CI = 1.2-8.0). This study provides evidence of genetic susceptibility to recurrent dysmenorrhea.