The association between exercise-induced bronchoconstriction (EIB) and exhaled nitric oxide (FE(NO)) has not been investigated in young children with atopic or non-atopic wheeze, two different phenotypes of asthma in the early childhood. Steroid naïve 3- to 7-yr-old children with recent wheeze (n = 84) and age-matched control subjects without respiratory symptoms (n = 71) underwent exercise challenge test, measurement of FE(NO) and skin prick testing (SPT). EIB was assessed by using impulse oscillometry, and FE(NO) by standard online technique. Although FE(NO) levels were highest in atopic patients with EIB, both atopic and non-atopic wheezy children with EIB showed higher FE(NO) than atopic and non-atopic control subjects, respectively. In atopic wheezy children, a significant relationship between FE(NO) and the severity of EIB was found (r = 0.44, p = 0.0004), and FE(NO) was significantly predictive of EIB. No clear association between FE(NO) and EIB or predictive value was found in non-atopic wheezy children. Both atopic and non-atopic young wheezy children with EIB show increased FE(NO) levels. However, the association between the severity of EIB and FE(NO) is present and FE(NO) significantly predictive of EIB only in atopic subjects, suggesting different interaction between bronchial responsiveness and airway inflammation in non-atopic wheeze.