Eleven protease mutations have been associated with reduced susceptibility to darunavir (DRV). We examined the prevalence and covariates of these mutations in 2 populations. Thirty percent of 1175 Northern California patients and 24% of 2744 non-California patients in the Stanford HIV Drug Resistance Database had viruses with 1 or more mutations associated with resistance to DRV. In multivariate analyses, the number of DRV resistance-associated mutations depended on the number of previous protease inhibitors (PIs) administered and on amprenavir/fosamprenavir treatment. Most PI-treated patients should respond favorably to DRV-based salvage therapy.