Increasing awareness of the utmost need for the limited resources to be used more efficiently has called for economic evaluation of drug therapy. OBJECTIVES: This was to assess the cost effectiveness of some antimicrobial agents used in the treatment of sexually transmitted diseases (STD). These include doxycycline versus tetracycline for chlamydial infection, benzathine penicillin versus procaine penicillin for syphilis, and ceftriaxone versus spectinomycin for gonorrhoea. The choices were based on standard treatment guidelines and observed prescriptions. METHODS: Cost Effectiveness Analysis was used. The prescribed/dispensed prescriptions in STD clinic between 1997 and 1999 were reviewed retrospectively. Relevant information such as diagnosis, prescribed/dispensed drugs, dosage, duration of therapy, laboratory results, physician's remarks among others were obtained from patient case-notes and dispensed prescriptions. In conjunction with these, time and motion studies and standard cost accounting technique were used. The cost per defined daily dose (DDD) and the cost of therapy for each agent were calculated. The cost components include overhead costs, and cost of drug/disposables acquisition. The literature was reviewed for positive and negative consequences of the considered therapeutic options. Improvements in signs and symptoms as well as eradication of the implicated organisms are the outcome measures. Decision table was used in the effectiveness rating. These were compared using chi square analysis. RESULTS: The results showed that doxycycline, benzathine penicillin and ceftriaxone were more effective than their respective couinterparts in the treatment of stated infections. For example, doxycycline was N0.92 per unit effectiveness while tetracycline was N1.82 per uint effectiveness. Tetracycline is still widely used in the country. Alteration of some variables (cost and effectiveness rating) in favour of less cost effective option did not change the conclusion confirming that doxycycline is truly more cost effective. CONCLUSION: It is concluded that tetracycline should no longer be used except when doxycycline is not available. This equally applies to benzathine penicillin and ceftriaxone compared to their counterparts. However patients peculiarities and contraindications need to be considered at all times.