Background Diarrhoea presents a considerable health risk to young children and is one of the leading causes of infant mortality. Although proven cost-effective interventions exist, South Africa is yet to reach the Sustainable Development Goals set for the elimination of preventable under-five mortality and water-borne diseases. The rural study area in the Eastern Cape of South Africa continues to have a parallel health system comprising traditional and modern healthcare services. It is in this setting that this study aimed to qualitatively examine the beliefs surrounding and perceived quality of healthcare accessed for children’s acute diarrhoea. Methods Purposive sampling was used to select participants for nine focus-group-discussions with mothers of children less than 5 years old and 11 key-informant-interviews with community members and traditional and modern practitioners. The focus-group-discussions and interviews were held to explore the reasons why mothers seek certain types of healthcare for children with diarrhoea. Data was analysed using manual thematic coding methods. Results It was found that seeking healthcare from traditional practitioners is deeply ingrained in the culture of the society. People’s beliefs about the causative agents of diarrhoea are at the heart of seeking care from traditional practitioners, often in order to treat supposed supernatural causes. A combination of care-types is acceptable to the community, but not necessarily to modern practitioners, who are concerned about the inclusion of unknown ingredients and harmful substances in some traditional medicines, which could be toxic to children. These factors highlight the complexity of regulating traditional medicine. Conclusion South African traditional practitioners can be seen as a valuable human resource, especially as they are culturally accepted in their communities. However due to the variability of practices amongst traditional practitioners and some reluctance on the part of modern practitioners regulation and integration may prove complex. Electronic supplementary material The online version of this article (doi:10.1186/s12913-016-1911-7) contains supplementary material, which is available to authorized users.