Background: There is a shortage of human resources for health in Malawi. In addition there is an on-going scale up of HIV services in the ART clinics and staffing levels have not kept pace with the scale up. Health care workers are working in poorly resourced clinics. Workload and limited resources are risk factors for the psychological condition burnout. Burnout causes turnover and diminished health and reduces efficiency. Burnout threatens the achievement of gaining universal access to HIV care in Malawi. Objectives: The overall objective of this study was to assess the magnitude of burnout and associated factors in health care workers in ART clinics in Blantyre, Malawi. The first specific objective was to find the prevalence of burnout among health care workers in ART clinics in Blantyre. The second specific objective was to identify factors that were associated with burnout among health care workers in ART clinics in Blantyre. Methods: Health care workers in 22 ART clinics in Blantyre District were given a self administered questionnaire for assessment of burnout and related factors. The clinics were a mix of rural and urban, public, private and CHAM facilities. Results: 132 health care workers responded to the questionnaire (81.5% response rate). They experienced moderate levels of burnout on the subscale emotional exhaustion and low levels of burnout on the subscales depersonalization and personal accomplishment. Factors that many participants found problematic and that were associated with higher levels of emotional exhaustion were: dissatisfaction with the hours they worked, feelings of having more responsibility than they could handle and having worries about transmission of TB. Factors that many participants found problematic and that were associated with higher levels of depersonalization were feelings of having more responsibility than they could handle and having worries about transmission of HIV. Participants who often provided home based care and participants who thought they had a good manger also had higher levels of depersonalization. Participants who did not have a job description or were dissatisfied with their work schedule had higher levels of burnout on the subscale personal accomplishment. To spend many hours getting water for the household was also associated with higher levels of burnout on the subscale personal accomplishment.