In this short article the authors review important factors which influence the composition of the gut microbiome in early infancy. They then look at evidence for a “gut-lung axis" in the progression of chronic lung disease in children. They report that gut microbial composition is associated with disease progression in cystic fibrosis (CF) and development of childhood asthma. The authors also reviewed the use of prebiotics, probiotics and synbiotics (a combination of pre- and probiotics) in lung disease in children. They found that whilst in animal studies Lactobacilli have immunoregulatory effects on the lung, results of human clinical trials were variable, possibly due to the specific bacterial strains used. They report that clinical data are missing for probiotic intervention in the development of asthma. For CF, three randomised controlled trials found a beneficial effect of probiotics, in particular Lactobacillus GG and Lactobacillus reuteri, in disease progression and activity.