The aim of this study was to correlate results of therapeutic drug monitoring, genotypic resistance and viral response to lopinavir/ritonavir (LPV/r) or saquinavir/ritonavir (SQV/r) containing antiretroviral regimens. The retrospective short-term study included 20 patients with LPV/r and 20 patients with SQV/r containing highly active antiretroviral therapy (HAART). At baseline 7 LPV/r patients and 10 SQV/r patients had CD4+T cell counts above 410 cells/microl. After 6 months CD4+T cells had doubled in 5 LPV/r and 2 SQV/r patients. In LPV/r patients the mean serum concentration of lopinavir (LPV) was 2.6 ppm and 67% of all LPV/r samples had 50 or fewer viral copies/ml. In SQV/r patients the mean serum concentration of saquinavir (SQV) was 2.1 ppm. 79% of all SQV/r samples had 50 or fewer viruses/ml. Pharmacoenhanced regimens efficiently suppress human immunodeficiency virus type 1 (HIV-1) and the risk of developing resistance mutations is therefore reduced. The implementation of drug monitoring is an additional tool to determine optimal treatment conditions.