OBJECTIVES: Risk factors for loss to follow-up (LTFU) were assessed for people living with HIV (PLHIV) at various reference out-patient clinics (expertise level II) and hospitals (expertise level III) in Mali. METHODS: HIV-1-positive adults starting antiretroviral therapy (ART) in 2006-2013 were eligible for inclusion. Risk factors for LTFU, defined as no visit in the 6 months preceding the last database update, were assessed with the Cox model, taking into account the competing risks of transfer and death. Potential risk factors at the start of ART were demographic and socioeconomic variables, World Health Organization (WHO) stage, CD4 count, period of ART initiation, type of ART, region of care, expertise level and distance from home. RESULTS: We included 9821 PLHIV, 33% of whom were male, starting ART at nine out-patient clinics and seven hospitals [five and two in the capital Bamako and four and five in the 'regions' (i.e. districts outside the capital), respectively] with a median (interquartile range) CD4 count of 153 (56-270) cells/μL. Five-year cumulative incidences of LTFU, transfer and death were 35.2, 9.7 and 6.7%, respectively. People followed at Bamako hospitals > 5 km from home, at regional hospitals or at regional out-patient clinics < 5 km from home were at higher risk of LTFU than people followed at Bamako out-patient clinics, whereas people followed at regional out-patient clinics 5-50 km away from home were at lower risk for LTFU. Deaths were less frequent at hospitals, whether in Bamako or in the regions, than at Bamako out-patient clinics, and more frequent at regional out-patient clinics. CONCLUSIONS: Expertise level and distance to care were associated with LTFU. Stigmatization may play a role for PLHIV living close to the centres in the regions.