To begin to understand the pathogenesis of endometriomas, Hawkins et al. carried out the first transcriptome-microRNAome analysis of endometriomas and eutopic endometrium and used gene expression profiling on the same samples to determine functional targets for these microRNA. Specimens were collected from women undergoing clinically indicated gynecologic surgery for removal of an endometriotic mass and/or other benign indications. Specimens of endometrium were obtained from the uterine fundus at the time of hysterectomy at a distance from any uterine leiomyomata. Specimens of endometriomas were full-thickness 1 cm biopsies of the cyst wall and were isolated away from areas of obvious ovarian cortex.