Background: Tuberculosis infection control (TBIC) is rarely implemented in the health facilities in resource limited settings. Understanding the reasons for low level of implementation is critical. The study aim was to assess TBIC practices and barriers to implementation in two districts in Uganda.

Methods: We conducted a cross-sectional study in 51 health facilities in districts of Mukono and Wakiso. The study included: a facility survey, observations of practices and eight focus group discussions with health workers.

Results: Quantitative: Only 16 facilities (31%) had a TBIC plan. Five facilities (10%) were screening patients for cough. Two facilities (4%) reported providing masks to patients with cough. Ventilation in the waiting areas was inadequate for TBIC in 43% (22/51) of the facilities. No facility possessed N95 particulate respirators. Qualitative: Barriers that hamper implementation of TBIC elicited included: under-staffing, lack of space for patient separation, lack of funds to purchase masks, and health workers not appreciating the importance of TBIC.

Conclusion: TBIC measures were not implemented in health facilities in the two Ugandan districts where the survey was done. Health system factors like lack of staff, space and funds are barriers to implement TBIC. Effective implementation of TBIC measures occurs when the fundamental health system building blocks -governance and stewardship, financing, infrastructure, procurement and supply chain management are in place and functioning appropriately.