In 1994, the Pilot Accreditation Programme for South African Health Services was launched as a research and development programme in the Faculty of Medicine at the University of Stellenbosch under the directorship of Professor Stuart Whittaker. The programme grew rapidly and evaluation research showed that it was well received and perceived to be of considerable value to participating facilities.

The rapid expansion of the programme resulted in the perception that it was too big for a single department and not an appropriate function of the University.

The emergence of COHSASA as an independent, non-partisan unit was a logical development. In 1995, in a memorandum of agreement, the University of Stellenbosch transferred the accreditation copyright and obligations to COHSASA, which was registered as a not-for-profit organisation. It started operations from a small office in Pinelands, Cape Town in 1996.

Over the past 18 years, COHSASA has developed healthcare accreditation programmes for hospitals, sub-acute care, psychiatric facilities and programmes, primary health care clinics, ambulance services and medical emergency centres and general practitioners.