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BACKGROUND: Medecins Sans Frontieres (MSF) provides TB treatment in Galkayo and Marere in Somalia. MSF international supervisory staff withdrew in 2008 owing to insecurity but maintained daily communication with Somali staff. In this paper, we aimed to assess the feasibility of treating TB in a complex emergency setting and describe the programme adaptations implemented to facilitate acceptable treatment outcomes. METHODS: Routinely collected treatment data from 2005-2012 were retrospectively analysed. In multivariate analyses, factors associated with successful outcome (cure or completion versus failure, death and default) were assessed, including the presence of international supervisory staff. Informal interviews were conducted with Somali staff regarding programmatic factors affecting patient management and perceived reasons for default. RESULTS: In total, 6167 patients were admitted (34.8% female; median age 24.0 years [IQR 13.0-38.0 years]). Treatment success was 79% (programme range 69-87%). Presence of international staff did not improve outcomes (adjusted OR 0.85, 95% CI 0.66-1.09; p=0.27). Perceived reasons for default included being away from family, nomadic group, insecurity, travel cost, need to return to grazing land or feeling better. CONCLUSIONS: Despite the challenges, a high percentage of patients were successfully treated. Treatment outcomes were not adversely affected by withdrawal of international supervisory staff.