Severe AIDS dementia complex is now a rare clinical condition in resource-rich settings in HIV-1-infected patients with access to modern antiretroviral therapies. However, minor neurocognitive decline and central nervous system abnormalities have been reported in clinical studies assessing HIV-1-infected subjects on modern antiretroviral therapy with undetectable plasma HIV-RNA. Ongoing characterisation and monitoring of these abnormalities are crucial to aid our understanding and assess future interventions. New magnetic resonance imaging (MRI) techniques, provide a non-invasive mechanism to assess impaired brain function (functional MRI, fMRI) and detect changes in brain biochemistry (magnetic resonance spectroscopy, MRS). In this review, changes described by fMRI and MRS in HIV disease both in the pre- and post-combination antiretroviral therapy eras are summarised.