Combination antiretroviral therapy (cART) maintains virologic control in HIV patients, but may lead to neurotoxicity. By using neuroimaging and cellular microparticle quantification, we explore the effects cART may have in both acute and chronic HIV-infection. We find that cART treatment does reduce microparticle levels associated with neuroinflammation to those of controls. Further, microparticle levels and neuroimaging results strengthen assumptions about immune dysfunction in HIV infection. We demonstrate that cerebral blood flow and cerebrovascular reactivity can be used in conjunction with quantitative microparticle levels to study the effects of neuroinflammation and cART treatment in both acute and chronic HIV infection.