Asthma-related symptoms can manifest in children during the early years, but only some of the children will develop the disease. This feasibility study showed that it is possible to apply non-invasive markers (in urine, exhaled nitric oxide (FENO) and exhaled breath condensate (EBC)) in 3-year-old children, and evaluated the biomarkers in relation to health outcomes and potential modifiers. FENO was correlated with respiratory allergy, and was borderline significantly correlated with wheezing, but not with the asthma predictive index (mAPI). EBC pH and urinary 8-oxo-deoxyguanosine were not significantly correlated with these clinical outcomes. An EBC proteolytic peptide pattern was developed, which could distinguish between mAPI-positive and -negative children. Non-invasive biomarkers may become a promising tool for investigating respiratory health in children but further research is needed.