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Background Ambulatory, community-based care for multi-drug resistant tuberculosis (MDR-TB) has been found to be effective in multiple settings with high cure rates. However, little is known about patient preferences around models of MDR-TB care. Médecins Sans Frontières (MSF) has delivered home-based MDR-TB treatment in the rural Kitgum and Lamwo districts of northern Uganda since 2009 in collaboration with the Ministry of Health and the National TB and Leprosy Programme. We conducted a qualitative study examining the experience of patients and key stakeholders of home-based MDR-TB treatment. Methods We used semi-structured interviews and focus-group discussions to examine patients' perceptions, views and experiences of home-based treatment and care for MDR-TB versus their perceptions of care in hospital. We identified how these perceptions interacted with those of their families and other stakeholders involved with TB. Participants were selected purposively following a stakeholder analysis. Sample size was determined by data saturation being reached within each identified homogenous category of respondents: health-care receiving, health-care providing and key informant. Iterative data collection and analysis enabled adaptation of topic guides and testing of emerging themes. The grounded theory method of analysis was applied, with data, codes and categories being continually compared and refined. Results Several key themes emerged: the perceived preference and acceptability of home-based treatment and care as a model of MDR-TB treatment by patients, family, community members and health-care workers; the fear of transmission of other infections within hospital settings; and the identification of MDR-TB developing through poor adherence to and inadequate treatment regimens for DS-TB. Conclusions Home-based treatment and care was acceptable to patients, families, communities and healthcare workers and was seen as preferable to hospital-based care by most respondents. Homebased care was perceived as safe, conducive to recovery, facilitating psychosocial support and allowing more free time and earning potential for patients and caretakers. These findings could contribute to development of an adaptation of treatment approach strategy at national level. [ABSTRACT FROM AUTHOR]