Several studies have shown a strong association between atopic diseases and autism spectrum disorder (ASD). However, the risk of atopic diseases in individuals having ASD-affected siblings has never been investigated. This nationwide population-based cohort study included 2762 individuals with ASD-affected siblings and 11,048 controls. Diagnoses of atopic diseases, including asthma, atopic dermatitis, allergic rhinitis, and allergic conjunctivitis, were ascertained from 1996 or the birth data to the end of 2011. Individuals with ASD-affected siblings had a higher risk for asthma, atopic dermatitis, allergic rhinitis, allergic conjunctivitis, and multiple atopic diseases compared with controls. In conclusion, individuals with ASD-affected siblings were more likely than were the controls to develop atopic diseases, suggesting shared familial mechanisms underlying the two conditions.