We conducted a clinical trial to compare the efficacy and safety profile of two prostaglandin analogues, enprostil (35 micrograms twice daily) and misoprostol (200 micrograms four times daily) in the treatment of acute duodenal ulcers in 214 patients. The two agents healed approximately 80% and in excess of 90% of duodenal ulcers after 4 and 6 weeks' therapy, respectively. There was a significantly lower ulcer healing rate in both treatment groups in smokers compared with non-smokers (P < 0.05). However, daytime and nighttime ulcer pain relief was achieved in fewer than 50% of patients by either agent. Diarrhea, which occurred in more than 40% of patients, was the predominant side effect, and occurred mainly during the first 2 weeks of therapy with either agent. Nevertheless, this side effect was mild and self-limiting in the majority of patients. Both agents were found to be safe and well tolerated by the majority of patients. We conclude that these prostaglandin analogues are safe and effective duodenal ulcer healing agents. Furthermore, there was very little difference between enprostil and misoprostol. The limiting factors, however, for their routine use as ulcer healing agents are their low efficacy with regard to ulcer pain relief and the high incidence of diarrhea.