Over the last two decades, consequences of HIV infection of the CNS on disease severity and clinical neuropsychiatric manifestations have changed. These changes are due, in part, to improved control of peripheral infection by new anti-retroviral medications and more efficient CNS penetration of combination anti-retroviral therapies (cART). While the life spans of HIVinfected patients have been prolonged with successful cART, the spectrum of cognitive alterations observed in these patients has broadened. Recent studies report that there does not appear to be a single prototypical pattern of neuropsychological impairment associated with HIV, but rather it includes diverse manifestations. Some co-morbidities such as substance abuse or depression, likely play significant roles in the neuropsychiatric profiles of some HIV-infected patients. Newly recognized factors contributing to neurocognitive impairments include ageing and unanticipated side effects from cART. Likewise, disturbances in neuroendocrine functioning are emerging as potentially important contributors to HIV-associated neurocognitive alterations. A retrospective review of clinical data from a small cohort of HIV-infected patients admitted to the psychiatric unit of an inner city hospital indicates that thyroid stimulating hormone levels were abnormal in 27% of the patients. Our data from analyses of post-mortem tissues from HIV patients show for the first time HIV infection of the hypothalamus and altered levels of thyroid hormone processing enzymes. Decreased vasopressin and oxytocin immunoreactivity in hypothalamic neurons was also observed. Thus, HIV infection of the CNS may contribute to changes in hypothalamic hormone signaling, thereby resulting in abnormal hypothalamic-pituitary-thyroid axis feedback and neuropsychiatric dysfunction.