Paired plasma and intracellular samples were obtained from 12 HIV-infected adults taking raltegravir twice daily (b.i.d.), and after switching to once daily. With b.i.d. dosing, no plasma trough concentrations were below the IC95, in contrast to 33% for once daily dosing. Fifty percent of the once daily group had intracellular trough concentrations below the inhibitory concentration 95 (IC95), 25% in the b.i.d. group. Lower plasma and intracellular concentrations may contribute to inferior virologic suppression rates observed with once daily raltegravir dosing.