The development of resistance mutations and human immunodeficiency virus (HIV) RNA levels were compared in lymph nodes and plasma of patients receiving antiretroviral therapy. Ten HIV-positive patients receiving high-dose saquinavir monotherapy (3600 or 7200 mg/day) underwent 14 lymph node biopsies before and during therapy. HIV RNA levels and appearance of resistance mutations to saquinavir were determined in simultaneous lymph node and plasma samples. HIV RNA levels were found to be consistently higher (mean, 3.16 log RNA copies; SD, 1.04; range, 2.23-5.59) in lymph nodes than in simultaneous plasma samples. Saquinavir therapy resulted in a reduction in HIV RNA levels in both plasma and lymph nodes. The presence or absence of a resistance mutation to saquinavir at codons 48 or 90 of the HIV-1 protease gene was identical in 13 of 14 biopsies, suggesting that resistance mutations to saquinavir appear within close temporal proximity in lymph nodes and plasma.