The response to antiretroviral therapy in human immunodeficiency virus-infected patients is limited by the emergence of drug resistance. This resistance is a consequence of the high rate of HIV mutation, the high rate of viral replication (especially when potent multidrug therapies are not used or taken reliably), and the selective effect of these drugs, which favors emergence of mutations that can establish clinical drug resistance. The introduction of highly active antiretroviral therapy, which typically includes at least 2 nucleoside reverse transcriptase inhibitors and a protease inhibitor or a non-nucleoside reverse transcriptase inhibitor, for most treatment-naive patients results in a reduction of viral load below the limit of detection determined by currently available HIV RNA assays. It is this marked reduction that results in durable viral suppression, usually only possible by the simultaneous use of 3 or 4 drugs. The reverse transcriptase inhibitor components of highly active antiretroviral therapy are crucial for such benefits of combination therapy. Specific amino acid changes are associated with resistance to several reverse transcriptase inhibitors, but new mutation complexes have been observed that can confer broad cross-resistance within this class. Genotypic and phenotypic resistance assays to measure drug resistance are being developed, but refinements in both methodology and our ability to interpret the results of these assays are necessary before they are introduced into widespread clinical use.