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To determine the incidence of and factors associated with neurological disorders in a large Taiwanese cohort of HIV-infected persons with free access to highly active antiretroviral therapy (HAART).A retrospective population-based cohort study was conducted using the National Health Insurance Research Database for the years 2000–2010.We identified 13,316 HIV-positive persons from 2000 through 2010. We used direct standardization to calculate age-adjusted and sex-adjusted incidence rates based on the 2000 World Health Organization world standard population. Factors associated with neurological disorders were analyzed using a Cox proportional hazards model.The standardized incidence of neurological disorders among HIV-infected persons increased from 22.16 per 1000 person-years in 2000 to 25.23 per 1000 person-years in 2010. Cognitive disorders increased significantly from 0.36 per 1000 person-years in 2001 to 7.44 per 1000 person-years in 2010 (trend P < 0.001). The rate of neurological disorders increased with age ≥55 years [adjusted hazard ratios (AHRs) 2.54, 95% confidence interval (CI): 1.89 to 3.40], hypertension (AHR 1.41, 95% CI: 1.12 to 1.76), substance abuse (AHR 1.65, 95% CI: 1.36 to 2.02), opportunistic infection (AHR 1.76, 95% CI: 1.47 to 2.11), syphilis (AHR 1.27, 95% CI: 1.10 to 1.47), and emergency department visits >5 (AHR 2.41, 95% CI: 1.96 to 2.97). The incidence of neurological disorders was negatively associated with adherence to HAART (adherence ≥85% AHR: 0.79, 95% CI: 0.64 to 0.97).The rising incidence of cognitive disorders among HIV-positive persons highlights the need to provide routine neurological evaluations at clinical visits. Receiving HAART with adherence ≥85% contributes to a reduced risk of neurological disorders.