Neonatal sepsis and early antibiotic therapy affect bacterial colonisation and immune activation after birth. This could have implications for later risk of allergy and asthma. Using a validated questionnaire (International Study of Asthma and Allergies in Children, ISAAC), we screened for asthma and allergy in three cohorts (total n = 834; median age 12, range 7-23 years) with different perinatal exposures as regards infection and antibiotics. Asthma, but not hay fever, was more prevalent after neonatal sepsis with adjusted odds ratio (OR) 1.63 [95% confidence interval (CI) 1.04, 2.56] and early antibiotic therapy (OR 1.48 [0.93, 2.35]) as compared with a control group. There was a trend towards increased atopic eczema after neonatal sepsis (OR = 1.39 [CI = 0.98, 1.98]). We conclude that neonatal sepsis is associated with an increased risk for later development of asthma. Early antibiotic exposure may contribute to this association.