Chronic inflammatory airway diseases, including asthma and chronic obstructive pulmonary disease, are responsible for a large global disease burden. The recognition of airway disease phenotypes is important for the application of new therapies targeted at specific underlying biological mechanisms. Biomarkers are indicators of biological or pathogenic processes that are objectively measured. In airway disease, biomarkers will ideally provide predictive information regarding diagnosis, disease mechanisms, phenotypes, treatment responses and prognosis or future risk. Non-invasive biomarkers that aid phenotyping are crucial to the development of targeted and more efficacious treatment, leading to personalised approaches to airway disease management. Sputum and peripheral blood eosinophils and fractional exhaled nitric oxide (FeNO) are current examples of potential biomarkers. However, recent advances in technology have demonstrated the role for airway transcriptomics in biomarker discovery. This perspective piece discusses the need for biomarkers in airway disease, the use of eosinophil counts and FeNO as biomarkers, the use of transcriptomics for biomarker discovery, and the application of biomarkers in clinical and research settings. A combined approach incorporating clinical information with biological markers such as eosinophils, FeNO and inflammatory gene markers is likely to have the most success in predicting patient outcomes.