By studying changes in the clonal composition of HIV-1 populations during the first weeks of zidovudine (ZDV) treatment before the development of ZDV resistance-conferring mutations, we demonstrated previously a selective inhibition of nonsyncytium-inducing (NSI) HIV-1, even when present as coexisting population in individuals also harboring syncytium-inducing (SI) HIV-1. In this study, we observed the opposite in individuals receiving didanosine (ddI) treatment. In these individuals ( n ϭ 7) a median Ϫ 0.98 log change (range Ϫ 1.55-0.08) in infectious cellular SI load was observed, whereas the coexisting NSI load was only minimally affected (median Ϫ 0.15 log, range Ϫ 1.27-0.50; P ϭ 0.03). The virus phenotype-dependent treatment responses were independent of the clonal composition of HIV-1 populations at baseline. Individuals treated with a combination of ZDV and ddI revealed an equal decline of both NSI and SI infectious cellular load ( n ϭ 4; NSI: median Ϫ 1.55 log, range Ϫ 2.19 to Ϫ 1.45; SI: median Ϫ 1.47 log, range Ϫ 1.81 to Ϫ 0.86; P ϭ 0.56).To test the hypothesis that the previously reported optimal activation of ZDV and ddI in activated and resting T cells, respectively, in combination with the differential T cell tropism of NSI and SI HIV-1 is the basis for the observed virus phenotype specific efficacy of nucleoside analogs, we studied the effect of treatment with a protease inhibitor that does not require intracellular activation. Individuals receiving ritonavir ( n ϭ 4) indeed showed equal declines in NSI and SI infectious cellular load (NSI: median Ϫ 2.37 log, range Ϫ 2.59 to Ϫ 2.16; SI: median Ϫ 2.82 log, range Ϫ 3.14 to Ϫ 2.50; P ϭ 0.25). Our data suggest HIV-1 phenotype as an additional parameter in the design of optimal treatment regimens. (