Men who have sex with men (MSM) have a higher prevalence of common mental disorders (CMD), as compared with heterosexual men. HIV infection is independently associated with higher rates of CMD. Given this context, and the high background community prevalence of HIV in South Africa, MSM are at even greater risk of developing CMD. The aim of this research was to investigate neuropsychiatric symptoms and disorders in MSM who were referred for assessment and management of mental health problems, in an MSM Clinic in urban Cape Town, South Africa. Twenty-five men were screened using the MINI, AUDIT, DUDIT, and IPDE Screener. Depression, suicidality, as well as alcohol and drug use disorders were highly prevalent in this group (44, 56, 48, and 56 % respectively). The personality disorder screening was suggestive of a high prevalence of personality disorders. The high prevalence of neuropsychiatric disorders in this sample supports the idea that integrated mental health services are needed to address the complex needs of this population. Adequate input into the mental health needs of this population could reduce the potential for HIV acquisition and transmission, improve adherence to treatment and care, and ensure the provision a comprehensive health service for MSM.