Background: Whether use of acetaminophen and/or antibiotics in early life can cause allergic diseases in later childhood remains inconclusive. The objective of the present study is to investigate the temporal relationship between exposure to acetaminophen and/or antibiotics in early life and developing allergic diseases in later childhood using two independent birth cohorts derived from the National Health Insurance Research Database (NHIRD) in Taiwan. Method: The authors conducted a prospective birth cohort study using 263 620 children born in 1998 and 9910 children born in 2003, separately, from NHIRD. Exposure status of acetaminophen and/or anti-biotics and potential confounding factors were included in the analyses. Cox proportional-hazard models were applied to determine the temporal effect of acetaminophen and/or antibiotic exposure on developing allergic diseases. Results: We observed positive relationship between exposure to acetaminophen and/or antibiotics during the first year of life and the development of three examined atopic diseases in 1998 birth cohort [adjusted hazard ratio (aHR): 1.86 for both use of acetaminophen and antibiotics in atopic dermatitis (95%CI: 1.74 –1.98); aHR: 1.60 for both use in asthma (95%CI: 1.53 – 1.67); aHR: 1.61 for both use in allergic rhinitis (95%CI: 1.55 – 1.67)]. Similar results were observed in 2003 birth cohort. Conclusion: Our findings have provided suggestive evidence the temporal effect of exposure to antibiotics and/or acetaminophen influences the development of childhood common allergic diseases. Further functional studies and/or animal studies will be needed for better understanding underlying regulatory mechanisms on this important clinical/public issue.