Background Endometriosis is a frequent disorder in women of childbearing age. Standard medical and surgical treatments are often unsatisfactory. Shockwave therapy has been suggested as a possible novel treatment. There is no clinical data however to support this approach. This article describes the research protocol for a pilot interventional trial aiming to evaluate transvaginal low intensity shockwave therapy in women with endometriosis. Methods Adult women (anticipated N = 60) suffering from endometriosis will be randomly allocated in a 1:1 ratio to an intervention group and a control group. The intervention group will receive 4 sessions of transvaginal low intensity radial shockwave therapy. The control group will receive 4 sham procedures. Assessment will be carried at 1, 3 and 6 months. The primary endpoint is the visual analog score for pelvic pain. Conclusion This monocentric single blinded randomized controlled pilot trial will be the first to assess transvaginal low intensity shockwave therapy as a novel treatment for endometriosis. 2