Previous clinical and genetic studies have suggested autism spectrum disorders (ASDs) is associated with immunological abnormalities involving cytokines, immunoglobulins, inflammation, and cellular immunity, but epidemiological reports are still limited. Patients with ASDs were identified in the National Health Insurance Database from 1996 to 2010, and compared with age and gender-matched controls (1:4) in an investigation of the association between ASDs and allergic/autoimmune diseases. A total of 1596 patients with ASDs were identified, and were found to have a significantly higher prevalence of allergic and autoimmune diseases than the control group. Patients with ASDs had increased risks of asthma (OR = 1.74, 95%CI = 1.51-1.99), allergic rhinitis (OR = 1.70, 95%CI = 1.51-1.91), atopic dermatitis (OR = 1.52, 95%CI = 1.30-1.78), urticaria (OR = 1.38, 95%CI = 1.12-1.69) and type 1 diabetes (OR = 4.00, 95%CI = 1.00-16.00), and a trend toward increasing comorbidity with Crohn's disease (OR = 1.46, 95%CI = 0.90-2.35). Our results support the association between ASDs and allergic diseases, and autoimmune comorbidities (type 1 diabetes and Crohn's disease). Further basic study is required to elucidate the possible underlying mechanisms and roles of allergy immunity and autoimmunity in the etiology of ASDs. (Contains 2 tables.)