The ATP-binding cassette (ABC) superfamily consists of energy-dependent transporters which in many cases play crucial roles in physiological processes; indeed, mutations in several ABC transporter genes has been shown to cause inherited diseases such as cystic fibrosis. The involvement of ABC transporters in systemic xenobiotic protection has led to an examination of the influence of these transporters on drug pharmacokinetics (plasma levels), including a number of clinical studies in which transporter expression levels were associated with drug plasma levels in healthy subjects. Researchers have also demonstrated correlations between the presence of genetic polymorphisms in ABC transporters and altered drug pharmacokinetics. The impact of ABC transporters and their naturally occurring genetic variants on drug pharmacodynamics (pharmacological action) has been characterized to a lesser extent, in part because of the difficulties of quantifying the pharmacological actions of many drugs. In this dissertation, we focus on the pharmacodynamic effects of ABC transporter expression and function in peripheral, non-pharmacokinetic tissues such as adipose and lymphocytes, especially with respect to anti-HIV therapies.First, we describe the expression of a putative splice variant of the ABCB1 (P-glycoprotein) transporter in lymphocytes. This half-sized protein functioned similarly to the classic full-size P-glycoprotein, but displayed altered immunoreactivity. ABCB1 RNA transcripts of approximately half the length of normal ABCB1 transcripts were found in lymphocytes from healthy subjects. The putative P-glycoprotein splice variant was detected in both HIV-negative and -positive subjects, indicating that it could influence the pharmacodynamics of anti-HIV drugs which have been classified as substrates of P-glycoprotein. We also investigated the effects of exposure to the HIV protease inhibitors atazanavir and saquinavir on the expression of lymphocyte P-glycoprotein. We found that in several subjects, the amount of P-glycoprotein expression increased substantially, suggesting that while there is no detectable generalized change in lymphocyte P-glycoprotein expression following atazanavir/saquinavir exposure, there may be genetic or environmental influences which affect the extent of lymphocyte P-glycoprotein induction in certain individuals.We also examine the roles that polymorphisms in candidate genes play in patient response to anti-HIV medications. These genes include the drug-metabolizing enzyme cytochrome P450 2B6, the xenobiotic transporters ABCB1 and ABCC4, and the inflammatory cytokine TNF. We performed this study in HIV-infected populations in San Francisco and Uganda, and found no significant associations between any of the polymorphisms investigated and patient virologic or immunologic response to antiretroviral therapies. We also characterized the ancestral admixture of the San Francisco cohort and determined that the minor allele frequencies of several of the polymorphisms differed between ethnicities.Last, we describe the effects of the adipose RNA expression of the transporter genes ABCC4 and SLC29A1, which regulate cellular exposure to the nucleoside analogue-based HIV reverse transcriptase inhibitors, on the development of lipodystrophy, a fairly common side effect of this class of anti-HIV therapies. Lipodystrophy is thought to result from mitochondrial toxicity, specifically the inhibition of the mitochondrial DNA polymerase. Indeed, we found that the nucleoside analogue fialuridine inhibited mitochondrial DNA synthesis in vitro; the effects of transporters in this system remain inconclusive. While we did not see any correlation between adipose transporter expression and the occurrence of lipodystrophy, we identified a genetic polymorphism in ABCC4 that was significantly associated with the development of lipodystrophy following stavudine treatment in a San Francisco population of HIV-infected individuals. It is possible that screening for this polymorphism may help to predict which patients will develop lipodystrophy following nucleoside analogue exposure.In general, the results described in this dissertation indicate that ABC transporters in lymphocytes and adipocytes may have important pharmacodynamic functionalities, as they modulate the intracellular concentrations of certain drugs. In particular, we have focused on HIV antiretroviral therapies because they exert pharmacological effects (beneficial or detrimental) in these cell types. Finally, we show that genetic variation in ABC transporters may be an important factor which determines how a patient responds to an antiretroviral regimen. Future studies should expand on this work with mechanistic studies to further unravel the role that transporters play in antiretroviral action, as well as carefully designed clinical studies to ascertain the validity of the pharmacogenetic associations reported here.