OBJECTIVES To perform a comparative cost-effectiveness analysis from the Brazilian Public Health System's perspective of the standard treatment with goserelin acetate of only patients with deep endometriosis confirmed by videolaparoscopy versus empirical treatment with goserelin acetate of all patients with chronic pelvic pain and suspected deep endometriosis. METHODS To determine the local experience of standard treatment and empiric treatment, it was conducted a specialist consult with a gynecologist from a public institution, with large experience in endometriosis treatment. It was developed an analytic decision model to estimate the cost effectiveness ratio of empiric treatment versus pattern treatment with goserelin depot 3.6 mg every four weeks, during six months. Efficacy rates were obtained from published literature. The model includes only direct costs, obtained from Ambulatory and Hospital Information System and Price Database of Brazilian Ministry of Health. The outcome used was time until symptoms improvement. RESULTS The cost-effectiveness analysis revealed that the empiric therapy with goserelin lead to a reduction of time until improvement of symptoms of 3 months, and lower cost with a reduction of US$1662 (1US$=R$1.6428), when compared to the pattern treatment with previous videolaparoscopy. CONCLUSIONS Empiric therapy of endometriosis using goserelin acetate seems to be a cost-saving alternative in the Brazilian Public Health System scenario