A previous survey had shown a high level of psychiatric morbidity among human immunodeficiency virus (HIV)-infected individuals, but the number of patients that are actually identified as having a psychiatric disorder in the medical service in Taiwan is unknown. Using the claims data of a nationally representative cohort from the Taiwan National Health Insurance Research Database, the diagnoses of psychiatric disorders among newly diagnosed HIV-infected individuals were investigated from 1998 through 2006. Two hundred and seventy-four (23.8%) of 1153 newly diagnosed HIV-infected patients were identified as having psychiatric disorders, with an average latency of 3.33±2.47 years after HIV infection. Anxiety and depressive disorders were the leading diagnoses. Male patients had lower morbidity (21.0% vs. 25.3%, p=0.056), but a shorter latency to be identified with a psychiatric disorder (2.1±2.13 vs. 3.9±2.40 years, p<0.001) than females. This first population-based cohort study showed a high morbidity of psychiatric disorders among HIV-infected individuals, but with a long latency after infection, and a gender effect was noted. Regular psychiatric evaluation and follow-up and prompt intervention are necessary for HIV-infected individuals.