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Conducting a phase III trial of a vaginal microbicide in a developing country poses several important and complex ethical challenges. As part of a process to bridge the gap between ethical theory and practice, we share our experiences in performing a phase III trial of Col 1492 (Advantage S) among female sex workers at four sites world-wide; Durban, Abidjan, Cotonou and Hat Yai. The ethical challenges included: (i) difficulties in obtaining informed consent. Participants were unable to grasp the concepts of a clinical trial for several weeks to months. In Cotonou, 30% of the women did not know the gel was tested for HIV prevention. Only 25% understood what a placebo was. In Durban, 70% of the women did not fully understand the study after 3 months; (ii) in sustaining the use of known HIV prevention strategies. Participants at the Durban site had difficulty in sustaining condom use due to financial and client preferences. Sex without condoms was worth more ($20) than sex with condoms ($10); (iii) in maintaining the confidentiality of the subject's HIV status. Novel approaches such as role plays and emphasis on other exclusion criteria were needed to maintain the confidentiality of women not included in the trial due to their HIV status; (iv) in providing care and support to the subjects who became infected with HIV during the trial. Women could only be offered routine sexually transmitted disease treatment and counselling. Anti-retrovirals were not offered. The successes and failures of the solutions attempted are described.