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Background  Good quality clinical practice guidelines (CPGs) are a vehicle to implementing evidence into allied health (AH) care. This paper reports on the current ‘state of play’ of CPGs in a lower-to-middle-income country (South Africa), where primary healthcare (PHC) AH activities face significant challenges in terms of ensuring quality service delivery in the face of huge PHC need.    Methods  A qualitative study was conducted, using semi-structured interviews with purposively-sampled individuals involved in AH PHC CPGs in South Africa. They included national and state government policy-makers, academics and educators, service managers, clinicians, representatives of professional associations, technical writers, and members of informal professional networks. The interview data was transcribed and de-identified, and analysed descriptively by hand-coding. The COREQ statement guided study conduct and reporting. A framework to guide research in other countries into perspectives of AH PHC CPG activities was established.    Results  Of the 32 invited, 29 people participated: of these 25 were interviewed and four provided meeting notes. Most participants had multiple professional roles, being engaged concurrently in clinical practice, academia, professional associations and / or government. Key themes comprised Players (sub-themes of sampling frame, participants, advice, role players and collaboration); Guidance (sub-themes of nomenclature, drivers, purpose, evidence sources) and Role of AH in PHC (sub-themes of discipline groupings, disability and rehabilitation, AH recognition).    Conclusion  There was consistently-expressed desire for quality guidance to support better quality AH PHC activities around the country. However no international CPGs were used, and there were no South African CPGs specific to local PHC AH practice. The guidance gap was filled by non-evidence-based documents produced often without training, to deal with specific clinical situations. This led to frustration, duplication and fragmentation of effort, confusing nomenclature, and an urgent need for standardised and agreed guidance. We provided a standardised framework to capture perspectives on CPGs activities in other AH PHC settings.    Electronic supplementary material  The online version of this article (10.1186/s12913-018-2837-z) contains supplementary material, which is available to authorized users.

South African primary health care allied health clinical practice guidelines: the big picture