The cellular landscape of the paediatric respiratory system remains largely uncharacterised and as a result, the mechanisms of globally important childhood respiratory diseases remain poorly understood. In this work we use paired bronchoalveolar lavage and blood sampling, combined with high dimensional flow cytometry, CITE-seq analysis, and inflammatory cytokine profiling, to map the immune cell landscape of the paediatric lung and comprehensively explore the local and systemic immune response in preschool aged children with pulmonary disease and age-matched healthy controls. This work highlights the utility of multiomic immune profiling to understand mechanisms of lung disease in childhood.