The majority of individuals infected with HIV, HBV or HCV live in resource limited settings. Over the last decade millions of patients in these settings have gained access to therapy, mostly specifically targeted to HIV. The first results of these treatment programmes are promising: the use of HAART can result in effective suppression of different HIV subtypes with consequent recovery of the patient’s immune system. However, successful treatment and monitoring protocols from the West have been adjusted because of budget and logistic constraints. Evaluation is essential to learn about the consequences for long-term viral efficacy and selection of resistance.