We report on rates of patient retention and attrition in the context of scaling-up antiretroviral treatment (ART) within a district hospital and its primary health centres in rural Malawi. 'Retention' was defined as being alive and on ART or transferred out, whereas 'attrition' was defined as died, lost to follow-up or stopped treatment. A total of 4074 patients were followed-up for 1803 person-years: 2904 were at the hospital and 1170 at health centres. Approximately 85% of patients were retained in care, both at hospital and health centres, with a retention rate per 100 person-years of 185 and 211, respectively [adjusted hazard ratio (HR) 1.18, 95% CI 1.10-1.28, P=0.001). Attrition rates per 100 person-years were similar: 33 and 36, respectively (adjusted HR 1.17, 95% CI 0.97-1.4, P=0.1). At health centres the incidence of loss to follow-up was significantly lower than at the hospital (adjusted HR 0.24, P<0.001, risk reduction 77%), but the rate of reported deaths was higher at health centres (adjusted HR 2.2, 95% CI 1.76-2.72, P<0.001). As Malawi continues to extend the coverage (and equity) of ART, including in rural areas, attention is needed to reduce losses to follow-up at hospital level and reduce mortality at primary care level.