Throughout South Africa, primary clinical care is mainly provided by nurses. In line with this, most professional nurses of the former Bloemfontein local authority completed a one year "Advanced Diploma in Health Assessment, Diagnosis and Treatment" course at the University of the Free State. This study aimed to compare the clinical competencies of nurses who obtained this diploma with those who did not. The primary objective was to assess the clinical management of one chronic and one acute disease (diabetes mellitus and acute respiratory tract infections in adults, respectively) for these two groups of nurses. Relationships between quality of care and nurses' and clinics' characteristics were also examined since they could be predictors of quality of care, independent of the influence of training. We reviewed records of 286 consecutive visits for adults with diabetes and 293 consecutive visits for adults with an acute respiratory tract infection (ARTI). Nurses completed questionnaires on nurse characteristics, while the researchers obtained the information about the clinics. Recording of important generic (for ARTIs) and disease-specific steps (for diabetes) in patient management were assessed. Results for patients of "trained" and "non-trained" professionals were compared and adjusted for nurses', clinics' and patients' characteristics. There was generally little evidence of patients being thoroughly managed. Formal training was marginally associated with better care for ARTIs (p = 0.06) but not for diabetes (p = 0.47). Other factors associated with more thorough care were years of experience in curative primary health care (p = 0.006) and additional nursing degrees for ARTIs (p = 0.03) and the presence of enrolled or assistant nurses at the clinic for diabetes (p = 0.06). Fixed clinics generally performed better than mobile and satellite clinics.