Endometriosis is a common gynecological disease often resulting in chronic pelvic pain and infertility. The pathogenesis of endometriosis is likely multifactorial and several hypotheses have been suggested to explain the presence of ectopic endometrial tissue and stroma. There is a growing body of evidence indicating that miRNA is involved in the etiology of endometriosis, so this study explored the possible roles of Dicer and Drosha in endometriosis formation. Paired eutopic and ectopic endometrium in ovarian endometriosis was collected and cultured. Quantitative RT-PCR and Western blot of pairs of eutopic and ectopic endometrium demonstrated mRNA and protein levels for Dicer and Drosha in ectopic endometrium (EC) were decreased significantly compared with eutopic endometrium (EU). When transfected with Dicer or Drosha small hairpin RNA (shRNA) in EU, a significant increase in cell proliferation and decreased in cell apoptosis was detected. Furthermore, the Bcl2 was increased and Bax was deceased. In comparison, a scramble siRNA transfection did not affect protein levels for these molecules. Results demonstrate the low expression of Dicer and Drosha significantly correlates with EC, and shDicer or shDrosha can affect cell proliferation and apoptosis, manipulating Dicer and Drosha in EC may result in novel treatment strategies for EMs.