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Background  Non-communicable diseases (NCDs) are increasing in prevalence in low-income countries including Uganda. The Uganda Ministry of Health has prioritized NCD prevention, early diagnosis, and management. However, research on the capacity of public sector health facilities to address NCDs is limited.    Methods  We developed a survey guided by the literature and the standards of the World Health Organization Pacakage of Essential Noncommunicable Disease Interventions for Primary Health Care in Low-Resource Settings. We used this tool to conduct a needs assessment in 53 higher-level public sector facilities throughout Uganda, including all Regional Referral Hospitals (RRH) and a purposive sample of General Hospitals (GH) and Health Centre IVs (HCIV), to: (1) assess their capacity to detect and manage NCDs; (2) describe provider knowledge and practices regarding the management of NCDs; and (3) identify areas in need of focused improvement. We collected data on human resources, equipment, NCD screening and management, medicines, and laboratory tests. Descriptive statistics were used to summarize our findings.    Results  We identified significant resource gaps at all sampled facilities. All facilities reported deficiencies in NCD screening and management services. Less than half of all RRH and GH had an automated blood pressure machine. The only laboratory test uniformly available at all surveyed facilities was random blood glucose. Sub-specialty NCD clinics were available in some facilities with the most common type being a diabetes clinic present at eleven (85%) RRHs. These facilities offered enhanced services to patients with diabetes. Surveyed facilities had limited use of NCD patient registries and NCD management guidelines. Most facilities (46% RRH, 23% GH, 7% HCIV) did not track patients with NCDs by using registries and only 4 (31%) RRHs, 4 (15%) GHs, and 1 (7%) HCIVs had access to diabetes management guidelines.    Conclusions  Despite inter-facility variability, none of the facilities in our study met the WHO-PEN standards for essential tools and medicines to implement effective NCD interventions. In Uganda, improvements in the allocation of human resources and essential medicines and technologies, coupled with uptake in the use of quality assurance modalities are desperately needed in order to adequately address the rapidly growing NCD burden.    Electronic supplementary material  The online version of this article (10.1186/s12913-018-3426-x) contains supplementary material, which is available to authorized users.

Capacity of Ugandan public sector health facilities to prevent and control non-communicable diseases: an assessment based upon WHO-PEN standards