The traditional end-points for clinical studies of lung diseases were based on functional parameters. Their value as surrogate markers for disease activity and progression has been increasingly questioned by scientists, carers, regulatory agencies and funding bodies. Novel tools and methods with regard to biomarkers and patient-reported outcomes have made these parameters emerge from their status as interesting secondary end-points and become potential primary outcomes for clinical trials. Nevertheless, their relevance and validity still needs to be proven. This issue of the European Respiratory Monograph describes the current status regarding end-points in all relevant areas of pulmonary medicine.