The objective of this study was to investigate the effect of initiating a salvage-therapy regimen on resistant viruses in heavily treated patients infected with human immunodeficiency virus type 1 (HIV-1). Nineteen patients receiving multiple antiretroviral drugs were tested for HIV-1 mutations associated with drug resistance by using an in-house method at baseline and at weeks 2, 4, and 8 of the salvage-therapy regimen. For the majority of mutations analyzed, the mean number of detectable mutations at baseline was significantly higher than the mean at weeks 2, 4, and 8 of salvage therapy. Introducing new and more potent therapy reduces the number of detectable drug resistance-associated mutations within 8 weeks, and no evidence was found that the new therapy promoted the emergence of novel mutations.