Few epidemiological studies have compared the risk factors of asthma or wheezing between atopic and non-atopic children. The objective of this study was to determine if there are specific risk factors for current wheezing related to atopic status in schoolchildren. Schoolchildren 9–12 yr of age from three Spanish cities (n = 2720) were subject to a cross-sectional study of asthma risk factors (by questionnaire) and atopy (by skin prick test) according to the ISAAC phase-II protocol. Risk factors for current wheezing (in the last 12 months) as reported by parents were investigated among the atopic (positive prick test to at least one allergen) and the non-atopic (negative prick test) children. The prevalence of current wheezing was 13.1% in the whole group, 22.1% in the atopic group and 7.8% in the non-atopic group. However, only 62.4% of children with current wheezing were atopic. Male gender and asthma in the mother and/or the father were both significant and independent risk factors for current atopic wheezing, whereas maternal smoking in the first year of the child's life and mould stains on the household walls were for current non-atopic wheezing. In summary, this study shows that atopic and current non-atopic wheezing children in Spain do not share identical environmental and family risk factors.