OBJECTIVES: Monitoring and evaluation of national antiretroviral therapy (ART) programs is vital, but routine, standardized assessment of national ART patient monitoring systems has not been established. Malawi has undertaken an ambitious ART scale-up effort, with over 57,000 patients initiated on ART by June 2006. We assessed the national ART monitoring and evaluation system in Malawi to ensure that the response to the epidemic was being monitored efficiently and effectively, and that data collected were useful. METHODS: The evaluation, performed in August 2005, generally followed the Updated Guidelines for Evaluating Public Health Surveillance Systems (CDC) and Interim Patient Monitoring Guidelines for HIV Care and ART (WHO). Assessment was conducted with qualitative methods, including twelve ART site visits, with standardized key informant interviews with ART clinic coordinators, clinical staff, and data managers, at each site. Meetings were also held with key governmental stakeholders, including Ministry of Health and National AIDS Commission. RESULTS: The national monitoring and evaluation system devised by the Ministry of Health HIV/AIDS Unit is successful in achieving its objectives, and facilitates important aspects of the national response to HIV. Several basic changes in the data collection tools and system would facilitate more effective long-term assessment of the ART program and support improved patient care. As the number of ART sites and patients continues to expand, the current manual paper-based system may be overwhelmed. Identification and implementation of a feasible electronic data system that would maintain and improve data quality and the efficiency of data recording and reporting and enhance patient care is a priority. CONCLUSIONS: The assessment of ART monitoring and evaluation systems can optimize the effectiveness of national ART programs, and should be considered in other resource-constrained countries rapidly scaling up ART.