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Background  Since its inception, the Uganda National Drug Authority (NDA) has regularly inspected private sector pharmacies to monitor adherence to Good Pharmacy Practices (GPP). This study reports findings from the first public facility inspections following an intervention (SPARS: Supervision, Performance Assessment, and Recognition Strategy) to build GPP and medicines management capacity in the public sector.    Methods  The study includes 455 public facilities: 417 facilities were inspected after at least four SPARS visits by trained managerial district staff (SPARS group), 38 before any exposure to SPARS. NDA inspectors measured 10  critical , 20  major,  and 37  minor  GPP indicators in every facility and only accredited facilities that passed all 10 critical and failed no more than 7 major indicators. Lack of compliance for a given indicator was defined as less than 75 % facilities passing that indicator. We assessed factors associated with certification using logistic regression analysis and compared number of failed indicators between the SPARS and comparative groups using two sample t-tests with equal or unequal variance.    Results  57.4 % of inspected facilities obtained GPP certification: 57.1 % in the SPARS and 60.5 % in the comparative group (Adj. OR = 0.91, 95 % CI 0.45–1.85,  p  = 0.802). Overall, facilities failed an average of 10 indicators. SPARS facilities performed better than comparative facilities (9 (SD 6.1) vs. 13 (SD 7.7) failed indicators respectively;  p  = 0.017), and SPARS supported facilities scored better on indicators covered by SPARS. For all indicators but one minor, performance in the SPARS group was equal to or significantly better than in unsupervised facilities. Within the SPARS (intervention) group, certified facilities had < 75 % compliance on 7 indicators (all minor), and uncertified facilities on 19 (4 critical, 2 major, and 13 minor) indicators.    Conclusions  Half of the Ugandan population obtains medicines from the public sector. Yet, we found only 3/5 of inspected public health facilities meet GPP standards. SPARS facilities tended to perform better than unsupervised facilities, substantiating the value of supporting supervision interventions in GPP areas that need strengthening. None compliant indicators can be improved through practices and behavioral changes; some require infrastructure investments. We conclude that regular NDA inspections of public sector pharmacies in conjunction with interventions to improve GPP adherence can revolutionize patient care in Uganda.    Electronic supplementary material  The online version of this article (doi:10.1186/s40545-016-0068-4) contains supplementary material, which is available to authorized users.

journal of pharmaceutical policy and practice

First regulatory inspections measuring adherence to Good Pharmacy Practices in the public sector in Uganda: a cross-sectional comparison of performance between supervised and unsupervised facilities