STDs are a significant public health problem in Brazil. A primary control strategy is the immediate treatment of symptomatic individuals. When services are unavailable, STD patients seek care in alternative settings. Probably the most frequently used settings are commercial pharmacies, where pharmacy clerks provide treatment, although Brazilian law prohibits selling antibiotics without prescription. Our objective was to evaluate prescribing practices by pharmacy clerks for STDs. We performed a cross-sectional study. Trained medical students visited 62 pharmacies in the city of Porto Alegre during March 2002. These were randomly chosen from a list of 863 registered pharmacies. The students presented to the pharmacy complaining of dysuria and urethral discharge. After obtaining a prescription, or not, they asked for additional instructions to be followed. Immediately after leaving the premises, the instructions were anonymously recorded. Of the 62 pharmacies visited, a clerk in 56 (90.3%, 95% confidence interval [CI]: 80.1%-96.4%) provided a prescription. Most frequently prescribed drugs were ampicillin with probenecide (29/51.8%) and rosoxacin (11/19.6%). Ministry of Health-recommended treatment was not suggested by any of the clerks. Forty-six additional recommendations were given. The use of condoms was the most frequent additional advice (42/46). Prescribing by pharmacy clerks is very prevalent in Porto Alegre. This may represent a lost opportunity for more comprehensive prevention effort (counselling, partner management, and diagnosing other STDs). Additionally, the most frequently prescribed drugs are not recommended by international or national health authorities for treatment of STDs, and none of these drugs covers chlamydia. We conclude that pharmacy clerks are a potentially important source of STD treatment and control but that their practices are in need of vast improvement.