Objectives: To test the effect of supplementing peer promotion of male condom use with clinic based counselling, measured in terms of STI prevalence and reported male condom use. Methods: 1000 female sex workers in Madagascar were randomised to two study arms: peer education supplemented by individual risk reduction counselling by a clinician (peer + clinic) versus condom promotion by peer educators only (peer only). STI testing was conducted at baseline and 6 months. Behavioural interviews were administered at baseline, 2, 4, and 6 months. Results: At baseline, women in the peer only arm had prevalences of 16.0%, 23.6%, and 12.1% for chlamydia, gonorrhoea, and trichomoniasis respectively, with an aggregate prevalence of 38.2%. Baseline STI prevalences for the peer + clinic arm were slightly lower and 34.1% in aggregate. At 6 months, aggregate STI prevalence increased in the peer only arm to 41.4%, whereas the aggregate prevalence diminished slightly to 32.1% in the peer + clinic arm. In logistic regression analyses, the estimated odds ratios (ORs) for chlamydia, gonorrhoea, trichomoniasis, and aggregate STI were 0.7 (95% confidence interval 0.4 to 1.0), 0.7 (0.5 to 1.0), 0.8 (0.6 to 1.2), and 0.7 (0.5 to 0.9) respectively, comparing the peer + clinic arm with the peer only arm. The logistic regression OR for reported condom use with clients in the past 30 days increased from 1.1 at 2 months to 1.8 at 6 months, comparing the peer + clinic arm with the peer only arm, and was 1.4 overall (1.1 to 1.8). Adjustment for baseline factors changed the regression results little. Conclusions: The impact of male condom promotion on behaviour can be heightened through more concentrated counselling on risk reduction. Persistently high STI prevalence despite increases in reported condom use by sex workers supports the need for multidimensional control programmes.