Early treatment of new-born high-risk children with certain probiotic strains has reduced the risk of atopic eczema. Whether probiotics reduce risk for airway inflammation in long term is not known. We aimed at studying the effect of probiotic treatment during the six first months of life on airway inflammation at age 5 yr. In a randomized double-blind allergy prevention trial between 2000 and 2007 in Helsinki, Finland, we gave a probiotic combination, plus pre-biotics, or placebo, to 1018 children during 6 months from birth. At age 5, we measured exhaled nitric oxide (FE(NO) ) in a randomized sub-population of 160 children. Allergic diseases and IgE-sensitization were assessed in all infants. FE(NO) did not differ between probiotic and placebo groups, median (interquartile range, IQR) 5.45 (4.3-7.3) vs. 5.70 (3.9-6.8) ppb, p = 0.22. FE(NO) was elevated among those suffering from asthma during the first 5 yr than in healthy non-sensitized children (p = 0.009). FE(NO) correlated positively with serum total and allergen-specific IgE concentrations. Early intervention with probiotics and pre-biotics does not affect airway inflammation later in childhood.