Background: The association between enterovirus infections in early life and risk of developing allergic diseases in children has remained unclear. We aimed to investigate the risk of allergic diseases (including: atopic dermatitis, asthma and allergic rhinitis) after enterovirus infection in children. Method: We conducted a retrospective cohort study using data collected from the National Health Insurance Research Database (NHIRD). Exposure status was defined as children with enterovirus infections during the first three years of life. Cox proportional hazards models with and without adjusting confounding factors were applied to determine temporal relationship between enterovirus infections and the development of childhood allergic diseases. Results: A total of 42 804 children were identified and examined in this study. Among them, 22 433 children were infected with enterovirus during the first three years of life. The results demonstrated that children infected with enterovirus during the first three years of life have an increased risk of atopic dermatitis, asthma and allergic rhinitis, respectively (adjusted hazard ratio (AHR): 1.70; 95% confidence interval (CI) = 1.50 – 1.92 for atopic dermatitis; AHR: 1.61; 95%CI = 1.51 –1.70 for asthma; AHR: 1.84; 95%CI = 1.75 –1.92 for allergic rhinitis). Conclusion: In sum, our findings suggest there is temporal relationship between enterovirus infection during the first 3 year of life and the elevated risk of developing childhood allergic diseases.