This qualitative study aims to assess health education practice in sexually transmitted infection (STI) clinics in South Africa with a view to develop improved health education programs in such clinics. Health workers' knowledge of and attitudes towards health education practice, their perceived health education skills, the content of health education in STI clinics and the organizational structure as context for health education were investigated. In-depth interviews were conducted with 18 health care workers practicing in the area of STI control. A lack in knowledge and skills required for effective health education practice was reported. The constraints posed by health workers' current knowledge and skills around health education and the organizational structure in terms of the absence of policy and protocols to govern health education, limited time, space and resources, impede on the actual practice of health education. It seems that these obstacles to health education facilitate a biomedical approach to STI management. This approach is further portrayed in the power dynamics between the health workers as well as between health workers and patients. The data suggest that a health education intervention needs to be directed at an individual level namely at health workers and at the organizational level, i.e. the clinic that provides the context for health education. The newly adopted district health system which equally embraces medical care and health promotion augers well for a holistic management of STIs in South Africa. This would ensure the recognition of all categories of health workers' contributions to health education within their own functions, strengths and time limitations.