Background: Improved clinic based syndromic management of sexually transmitted diseases (STDs) in Tanzania reduced HIV transmission. However, in many developing countries, people seek STD treatment in pharmacies. This study used standardised simulated patients (SSP) to assess STD syndromic management in pharmacies and evaluate the impact of an educational intervention. Methods: SSP presented syndromes of urethral discharge, genital ulcer, vaginal discharge, and pelvic inflammatory disease (PID) at 180 randomly selected pharmacies in Lima, Peru. These pharmacies were then randomised to receive or not receive education on STD recognition, management, and prevention counselling, and were again visited by SSP. Results: At 360 pharmacy visits before the intervention, syndromes most often recognised as STD related were genital ulcer (81%) and urethral discharge (73%) in men, followed by vaginal discharge (43 %) and PID (6 %) in women. Treatments offered to 82.5 % of SSP rarely conformed to international or national guidelines (for urethral discharge, 1.5%; genital ulcer, 1%; vaginal discharge, 4%; and PID, none). Only 20.5% of SSP were referred to a physician and 30% received any counselling. The intervention reached 55% of pharmacies, and produced a small but significant increase in counselling; by 'intent to intervene' analysis, intervention pharmacies provided post-counselling more often than did controls (40% v 27%, p = 0.01). Conclusion: Pharmacies usually failed to recognise STD syndromes in women, and usually provided treatment, most often with ineffective regimens. Educational interventions improved counselling. More effective interventions are needed to improve STD recognition, treatment, and referral practices.