• The M184V/ I mutation developed in 2/ 19 (10.5%) isolates analysed from patients in the emtricitabine/ tenofovir disoproxil fumarate/ efavirenz group and in 10/ 29 (34.5%) isolates analysed from the lamivudine/ zidovudine/ efavirenz group (p-value < 0.05, Fisher’ s Exact test comparing the emtricitabine+tenofovir disoproxil fumarate group to the lamivudine/ zidovudine group among all subjects). • No virus analysed contained the K65R mutation. • Genotypic resistance to efavirenz, predominantly the K103N mutation, developed in virus from 13/ 19 (68%) patients in the emtricitabine/ tenofovir disoproxil fumarate/ efavirenz group and in virus from 21/ 29 (72%) patients in the comparative group.