BACKGROUND: This study was conducted to compare the safety, effectiveness and acceptability of 400 mcg sublingual misoprostol and 600 mcg oral misoprostol for treatment of incomplete abortion. STUDY DESIGN: We used an open-label randomized controlled trial conducted from July 2005 to August 2006 in a large tertiary level maternity hospital in Antananarivo, Madagascar, and a large tertiary level hospital in Chisinau, Moldova. Three hundred consenting women seeking treatment for clinically diagnosed incomplete abortion with uterine size ≤12 weeks since last menstrual period were randomized to misoprostol either 600 mcg orally or 400 mcg sublingually. The primary outcome measure was the complete resolution of clinical signs and symptoms of incomplete abortion without need for surgical intervention. Women were seen for follow-up on Day 7 and, if necessary, on Day 14 to assess abortion status. The study was powered to detect a 7% difference in efficacy with a total of 142 women required in each arm. RESULTS: Efficacy rates were 94.6% and 94.5%, for the oral and sublingual routes, respectively (RR: 1.00, 95% CI=0.95–1.06, p=.98). At 1 week follow-up, more than 80% of women had completed abortions (77.8% oral and 84.8% sublingual, p=.12). Mean pain scores were 2.95 and 3.04, respectively, for the oral and sublingual groups. Side effects included abdominal pain, bleeding, headaches and dizziness/weakness with no differences reported between the two groups. Acceptability and satisfaction were high for both routes and women indicated a preference for medical versus surgical treatment if ever needed in the future. CONCLUSION: Both treatment regimens were very effective. Four hundred micrograms of sublingual misoprostol and 600 mcg oral misoprostol appear to have similar safety and effectiveness profiles when used for the treatment of incomplete abortion. A lower 400-mcg misoprostol dose may provide an alternative treatment option as well as have potential benefits in terms of cost.