Background: Estonia is among those Eastern European countries that have witnessed an explosive intravenous drug use-driven HIV epidemic. Early sexually transmitted disease (STD) diagnosis and appropriate treatment is essential to prevent an STD-driven HIV epidemic. Objectives: The objectives of this study were to define the schedule of antibiotic treatment doctors in Estonia used to treat STDs, and to determine if the treatments used correspond to evidence-based medicine treatment principles. Study Design: Using an administrative database of the Estonian Health Insurance Fund on pharmaceuticals reimbursement, we obtained information on: drug (ATC 1998) prescribed with an STD diagnosis (International Classification of Diseases and Related Health Problems, syphilis, gonorrhea, genital Chlamydia trachomatis and Trichomonas vaginalis infections, and genital herpes), prescribing physician specialty, and patient demographics (date of birth, gender). To evaluate the correspondence of STD treatment to evidence-based medicine principles, the therapeutic regimens used were compared with recommendations from the European Sexually Transmitted Infections Management Guidelines. Results: In 2001 and 2002, physicians ordered 17,077 prescriptions for systemic antibacterial medications to treat STDs in 12,823 different individuals: 2942 men (mean age, 31.8 years) and 9880 women (mean age, 29.5 years). The majority of STD treatments were prescribed by gynecologists (60%) or dermatovenerologists (29%); general practitioners treated 8% of STDs. In 11% of treatment episodes, the drug prescribed was inconsistent with guideline recommendations; additionally, in 9% of episodes, the recommended drug was chosen but the prescribed dose was too low. At least 20% of treatment episodes could therefore be considered inappropriate. Conclusions: Educational efforts are needed to increase physician awareness of evidence-based approaches for STD management and treatment to assure effective STD care.