Cytomegalovirus (CMV) affects γδ T-cell profiles in healthy individuals and transplant recipients, but the effects of HIV and CMV have not been distinguished in HIV patients. CMV-seropositive Indonesian HIV patients (n = 40) were studied before ART and after six months, alongside healthy controls (n = 20). 50% of patients started ART with detectable CMV DNA. Proportions of Vδ2 γδ T-cells were high in patients and declined on ART, whilst proportions of Vδ2 γδ T-cells were uniformly low, and correlated inversely with levels of CMV DNA and CMV-reactive antibody. Residual Vδ2 cells were enriched for markers of terminal differentiation, but this did not associate with CMV metrics. Patients with CMV DNA at baseline showed a direct correlation between CMV reactive-antibody and CD8 γδ T-cells. Our data are consistent with a role for CMV in the depletion of Vδ2 γδ T-cells in HIV patients beginning ART, with no consistent evidence of a role for CMV in γδ T-cell activation or differentiation.