A wide range of outcome measures or endpoints has been used in clinical trials to assess the effects of treatments in paediatric respiratory diseases. This can make it difficult to compare treatment outcomes from different trials and also to understand whether new treatments offer a real clinical benefit for patients. Clinical trials in respiratory diseases evaluate three types of endpoints: subjective, objective and health-related outcomes. The ideal endpoint in a clinical trial needs to be accurate, precise and reliable. Ideally, the endpoint would also be measured with minimal risk and across all ages, easy to perform, and be inexpensive. As for any other disease, endpoints for respiratory diseases must be viewed in the context of the important distinction between clinical endpoints and surrogate endpoints. The association between surrogate endpoints and clinical endpoints must be clearly defined for any disease in order for them to be meaningful as outcome measures. The most common endpoints which are used in paediatric trials in respiratory diseases are discussed. For practical purposes, diseases have been separated into acute (bronchiolitis, acute viral-wheeze, acute asthma and croup) and chronic (asthma and cystic fibrosis). Further development of endpoints will enable clinical trials in children with respiratory diseases with the main objective of improving prognosis and safety.