Solid organ transplantation in Human Immunodeficiency Virus 1 (HIV)-infected individuals requiring concomitant use of immunosuppressants (IS) [e.g., cyclosporine (CsA) or tacrolimus (TAC)] and antiretrovirals (ARVs) [e.g., protease inhibitors (PIs) and/or non-nucleoside reverse transcriptase inhibitors (NNRTIs)] is complicated by significant drug interactions. We describe the pharmacokinetics of CsA and TAC in 52 patients on both IS and NNRTIs, PIs, or combined NNRTIs+PIs, in studies conducted at 2 weeks, 3, 6, 12 and 24 months after transplantation. CsA and TAC blood concentrations were measured by LC/MS/MS. This multisubject, varied ARV-IS drug combination, longitudinal observational patient study provided a unique opportunity to examine the effect of different ARV drugs on IS PK by comparing ratios of parameters over time and between PK parameters. Subjects taking concomitant PIs exhibited increases in CsA and TAC exposure (AUC/dose) due to increased apparent oral bioavailability and decreased apparent oral clearance. Those subjects taking CsA and concomitant efavirenz (EFV) showed time dependent increases in exposure due to ~30% increases in apparent oral bioavailability over time as well as decreased apparent oral clearance, while subjects on TAC and EFV showed time-dependent changes in all PK parameters. The increased bioavailability was not observed in patients on CsA and nevirapine (NVP). These differences between IS drugs and the changes in PK parameters are not easily predicted, illustrating the importance of continued therapeutic drug monitoring in these patients on these complex medication regimens.