Although the human immunodeficiency virus (HIV) protease inhibitors are highly effective, they are characterized by low and/or variable bioavailability with limited penetration into the central nervous system (CNS). Their clinical use is limited by patient compliance and by drug-drug interactions. The effect of drug solubility on their oral absorption has been investigated but further evaluation of this relationship is required. First pass metabolism appears to be significant for the HIV protease inhibitors and they are extensively metabolized by cytochrome P450 (CYP) 3A4. Recent studies suggest that these drugs are substrates for the P-glycoprotein efflux pump, which can limit their intestinal absorption and their transport across the blood-brain barrier. Drugs inducing or inhibiting CYP3A4 and/or P-glycoprotein may influence the bioavailability of the HIV protease inhibitors. The low bioavailability, variable absorption and drug-drug interactions of the HIV protease inhibitors may be related to the variability of cytochrome P450 and P-glycoprotein expression and to possible CYP3A4/P-glycoprotein interactions. To improve oral HIV protease inhibitor therapy, it is essential to mechanistically characterize the cell specific, tissue specific and regional intestinal dependencies of drug transport, secretory transport, metabolism and P-glycoprotein/CPY3A4 interactions. This report reviews the physicochemical characteristics and pharmacokinetics of the HIV protease inhibitors while considering the relationships between their hepatic and intestinal metabolism, low bioavailability, variable absorption and drug-drug interactions.