INTRODUCTION: Although several studies have explored factors associated with loss to follow-up (LTFU) from HIV care, there remains a gap in understanding how these factors vary by setting, volume of patient and patients' demographic and clinical characteristics. We determined rates and factors associated with LTFU in HIV care Lilongwe, Malawi. METHODS: We conducted a retrospective cohort study of HIV-infected individuals aged 15 years or older at the time of registration for HIV care in 12 ART facilities, between April 2012 and March 2013. HIV-positive individuals who had not started ART (pre-ART patients) were clinically assessed to determine ART eligibility at registration and during clinic follow-up visits. ART-eligible patients were initiated on triple antiretroviral combination. Study data were abstracted from patients' cards, facility ART registers or electronic medical record system from the date of registration for HIV care to a maximum follow-up period of 24 months. Descriptive statistics were undertaken to summarize characteristics of the study patients. Separate univariable and multivariable poisson regression models were used to explore factors associated with LTFU in pre-ART and ART care. RESULTS: A total of 10,812 HIV-infected individuals registered for HIV care. Of these patients, 1,907 (18%) and 8,905 (82%) enrolled in pre-ART and ART care, respectively. Of the 1,907 pre-ART patients, 490 (26%) subsequently initiated ART and were included in both the pre-ART and ART analyses. The LTFU rates among patients in pre-ART and ART care were 48 and 26 per 100 person-years, respectively. Of the 9,105 ART patients with reasons for starting ART, 2,451 (27%) were initiated on ART because of pregnancy or breastfeeding (Option B+) status. Multivariable analysis showed that being ≥35 years and female were associated with decreased risk of LTFU in the pre-ART and ART phases of HIV care. However, being in WHO clinical stage 3 (adjusted risk ratio (aRR) 1.35, 95% confidence interval (CI): 1.20-1.51) and stage 4 (aRR 1.87, 95% CI: 1.62-2.18), body mass index ≤ 18.4 (aRR 1.24, 95% CI: 1.11-1.39) at ART initiation, poor adherence to clinic appointments (aRR 4.55, 95% CI: 4.16-4.97) and receiving HIV care in rural facilities (aRR 2.32, 95% CI: 1.94-2.87) were associated with increased risk of LTFU among ART patients. Being re-initiated on ART once (aRR 0.20, 95% CI: 0.17-0.22), more than once (aRR 0.06, 95% CI: 0.05-0.07), and being enrolled at a low-volume facility (aRR 0.25, 95% CI: 0.20-0.30) were associated with decreased risk of LTFU from ART care. CONCLUSION: A sizeable proportion of ART LTFU occurred among women enrolled during pregnancy or breast-feeding. Non- compliance to clinic and receiving ART in a rural facility or high-volume facility were associated with increased risk of LTFU from ART care. Developing effective interventions that target high-risk subgroups and contexts may help reduce LTFU from HIV care.