Health care worker (HCW) in Malawi may acquire HIV infection through occupational injuries, in particular since HIV prevalence among inpatients and incidence of occupational injuries are high. A post exposure prophylaxis (PEP) programme for occupational injuries at Queen Elizabeth Central Hospital (QECH) commenced in 2003. We performed an audit of this programme from 2003 through 2008. 203 Occupational injuries were reported. The majority were needle stick injuries (76.3%). Half of the clients were in a training position. A dual ART regimen was most frequently prescribed. Triple therapy use increased over time and was more frequent in expatriate students. Many nurses and clinical officers were not fully vaccinated for HBV. Based on previous incidence data, occupational injuries were likely to be underreported. Data on side effects were incomplete, however PEP discontinuation due to side effects occurred only twice. Follow up visits were poorly attended, therefore the efficacy of PEP could not be evaluated. Prevention efforts for occupational injuries should be increased and specifically target HCWs in training positions. Measures to improve quality of the PEP programme include effective publicity campaigns, compulsory Hepatitis B vaccination and active tracing of HCWs who default follow up after PEP.