Background: Very little is known about the influence of Highly Active Antiretroviral Therapy (HAART) on the surface expression of CCR5 and CXCR4 with respect to receptor tropism and replication kinetics of autologous HIV strains, during continuous therapy and structured treatment interruption (STI) regimens. Objectives: The main objectives of this study were to assess whether continuous therapy and STI regimens had any modulatory effects on expression of CCR5 and CXCR4 on T lymphocytes. Study Design: We studied 6 patients on continuous HAART, 4 patients on STI and 1 treatment-naïve patient. Sequential peripheral blood mononuclear cells (PBMC) samples were analyzed to determine viral replication kinetics, the genotype influencing tropism of the autologous strain, in vitro co-receptor usage patterns in relation to the surface expression of each co-receptor. Results: Our data suggest that predominant CCR5 expression and tropism, during therapy, but significant downmodulation of CXCR4 expression. During the off-therapy phases of STI, CXCR4 expression increased, which correlated with increased CXCR4 tropism of isolates from these time points. In-vitro tropism during therapy was consistent with the HIV-1 V3 genotype, which was characteristic of CCR5 using strains. Conclusions: These results suggest that certain HAART regimens influence the surface expression of CXCR4, which may have profound implications for antiretroviral treatment.