There is little information about disease conditions that are diagnosed in patients diagnosed as having World Health Organization Clinical Stage 3 HIV who are started on antiretroviral therapy (ART) in Africa. We therefore conducted an audit in the central region of Malawi of patients registered for ART between January and September 2006. There were 4299 patients in Stage 3 of whom 4154 had data about their disease conditions. Only one condition was listed for 3880 patients. Of these, 1892 (48.8%) had unexplained weight loss, chronic fever or chronic diarrhoea, 822 (21.2%) had active/previous tuberculosis (TB) and 671 (17.3%) had a severe presumed bacterial infection. No patient was diagnosed as having haematological abnormalities. Nearly half the patients started on ART had a symptomatic, unspecified disease, (which may be obscuring important pathologies such as TB) and almost no laboratory assessment had taken place before the commencement of ART. These two areas need to be addressed in order to improve the management of patients starting on ART.