Main text In BMC Medicine, a recent study utilizing gene expression data from endometriosis lesions demonstrates that ovarian endometrioma (OMA) subtype of endometriosis displays the most significant response to estrogen suppression treatment by directly affecting ESR2 3. To compare gene expression in endometrial samples, this study utilized genome-wide gene expression data from the University of Turku (Dataset A) and gene expression data from the Gene Expression Omnibus GSE141549, as well as data collected from European ancestry patients attending clinics at the Royal Women’s Hospital or Melbourne in-vitro fertilization in Melbourne (Dataset B). Additionally, the gene expression profiles remain consistent regardless of the menstrual stage; however, they are able to distinguish between different lesion subtypes, with OMA being significantly different from both SUP and DIE. ...the gene expression profile is altered by estrogen suppression medication in OMA, but not in SUP or DIE.