Purpose: To study the incidence and epidemiology of Behcet’s disease in Taiwan. Methods: This retrospective cohort study was conducted using the nationwide reimbursement database in Taiwan. One million registered beneficiaries of the Taiwan National Health Insurance system in 2000 were randomly selected. All medical claims of these persons were collected. The definition of having Behcet’s disease was based on diagnostic codes. Persons who had incomplete registry data or diagnoses prior to 2001 were excluded. Annual incidence between 2001 and 2011 was calculated and risk factors for incidence were explored using the Cox proportional regression model. Characteristics of patients with Behcet’s disease with and without uveitis were compared. Results: A total of 236 newly diagnosed patients with Behcet’s disease were found between 2001 and 2011. The average incidence was 2.40 cases per 100,000 person-years (ranging from 1.29 to 3.53). Female patients and those aged between 40 and 65 years were at the highest risk of Behcet’s disease. Only 18.2% of the patients had also suffered from uveitis. The subspecialties of doctors making initial diagnoses and the number of prescribed immunomodulatory agents differed significantly between the patients with and without uveitis (p < 0.001 and <0.05, respectively). Conclusion: Incidence of Behcet’s disease was not high in Taiwan and relatively few of the patients developed uveitis. Patients of working age or who were female were more likely to have Behcet’s disease. However, age of onset and clinical severity differed between patients with and without uveitis.