Widespread use of combination antiretroviral therapy for HIV has led to increased incidence of HIV resistance and a need for antiretroviral resistance testing to optimize therapeutic choices. Antiretroviral resistance analysis is performed using either genotypic or phenotypic assays. Genotypic assays identify resistance-associated mutations in the HIV genome. They are faster and less technically demanding than phenotypic assays; however, the associations between mutations and resistance patterns are often complicated, making interpretation difficult. Phenotypic assays directly measure the ability of antiviral compounds to inhibit replication of patient-derived virus. Phenotypic assays provide results that are easier to interpret; however, there is little data that relates the degree of resistance detected in phenotypic assays to patient clinical response. Despite limitations, the improved therapeutic outcome of therapies guided by resistance testing is leading to incorporation of resistance testing into the standard of care for HIV treatment.