STUDY QUESTION: Is the methylation status of the glutathione S-transferase M1 (GSTM1) promoter region altered in patients with ovarian endometriosis, and does this affect the expression of GSTM1 in their endometrial tissues? SUMMARY ANSWER: The promoter region of GSTM1 was significantly hypomethylated in the ectopic and eutopic endometrium of patients with ovarian endometriosis and this was associated with higher expression of GSTM1 mRNA. WHAT IS KNOWN ALREADY: GSTM1, a member of the glutathione S-transferase family, is primarily known as a detoxification enzyme, but it has also been shown to negatively regulate apoptosis-related signalling cascades through protein-protein interactions with apoptosis signal-regulating kinase-1. STUDY DESIGN, SIZE, DURATION: This is a case-control study between September 2013 and December 2016, involving 65 patients with ovarian endometriosis and 53 women without endometriosis. We analysed the methylation status and expression levels of GSTM1 in the ectopic and eutopic endometrium of patients with ovarian endometriosis and the endometrium of women without endometriosis. In addition, we collected endometrial samples from 12 women without endometriosis for endometrial epithelial cell cultures. PARTICIPANTS/MATERIALS, SETTING, METHODS: Methylation levels of the GSTM1 promoter region in the ectopic and eutopic endometrial tissues of patients with ovarian endometriosis and the endometrial tissues of women without endometriosis were analysed by pyrosequencing. The expression of GSTM1 mRNA and protein in endometrial tissues was investigated by RT-qPCR and immunohistochemistry, respectively. Primary cell culture, gene transfection, Cell Counting Kit-8 assay and flow cytometry were used to analyse the effect of GSTM1 on viability and apoptosis in endometrial epithelial cells. MAIN RESULTS AND THE ROLE OF CHANCE: Compared with that in the endometrium of women without endometriosis, the GSTM1 promoter region was significantly hypomethylated in the ectopic and eutopic endometrium of patients with ovarian endometriosis. Additionally, GSTM1 mRNA and protein levels were significantly higher in the ectopic and eutopic endometrium than in the control endometrium. Moreover, the methylation levels of the GSTM1 promoter region were significantly negatively correlated with the mRNA expression of GSTM1. Furthermore, in vitro results suggested that the over-expression of GSTM1 could significantly increase viability and inhibit apoptosis in endometrial epithelial cells following hormone treatment and withdrawal. LIMITATIONS, REASONS FOR CAUTION: Due to restrictions in the isolation and culture of pure populations of endometrial epithelial cells, as well as limitations in the number of passages possible in primary cells, we could not explore the underlying molecular mechanism by which GSTM1 modulates apoptosis in endometrial cells. WIDER IMPLICATIONS OF THE FINDINGS: This study provides new evidence to support the notion that endometriosis may be an epigenetic disease.