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Introduction: In 2016, South Africa's National Department of Health (NDOH) launched the National Adherence Guidelines for Chronic Diseases for phased implementation throughout South Africa. Early implementation of a 'minimum package' of eight interventions in the Adherence Guidelines for patients with HIV is being undertaken at 12 primary health clinics and community health centres in four provinces. NDOH and its partners are evaluating the impact of five of the interventions in four provinces in South Africa., Methods and Analysis: The minimum package is being delivered at the 12 health facilities under NDOH guidance and through local health authorities. The five evaluation interventions are: (1) fast track initiation counselling for patients eligible for antiretroviral therapy (ART); (2) adherence clubs for stable ART patients; (3) decentralised medication delivery for stable ART patients; (4) enhanced adherence counselling for unstable ART patients; and (5) early tracing of patients who miss an appointment by ≥5 days. For evaluation, NDOH matched the 12 intervention clinics with 12 comparison clinics and randomly allocated one member of each pair to intervention or comparison (standard of care) status within pairs, allowing evaluation of the interventions using a matched cluster-randomised design. The evaluation uses data routinely collected by the clinics, with no study interaction with subjects to prevent influencing the primary outcomes. Enrolment began on 20 June 2016 and was completed on 16 December 2016. A total of 3456 patients were enrolled and will now be followed for 14 months to estimate effects on short-term and final outcomes. Primary outcomes include viral suppression, retention and medication pickups, evaluated at two time points during follow-up., Ethics and Dissemination: The study received approval from the University of Witwatersrand Human Research Ethics Committee and Boston University Institutional Review Board. Results will be presented to key stakeholders and at international conferences and published in peer-reviewed journals., Trial Registration Number: NCT02536768; Pre-results., Competing Interests: Competing interests: None declared., (© Article author(s) (or their employer(s) unless otherwise stated in the text of the article) 2018. All rights reserved. No commercial use is permitted unless otherwise expressly granted.)