In patients with inflammatory diseases affecting the lungs, a variety of cytokines and mediators are present in the lining lining the airways. These biomarkers can provide a wealth of information about the disease including severity, activity and response to treatment. However, collecting samples is particularly challenging and methods such as bronchoscopy and alveolar lavage are too invasive for repeated use. Currently, there is ongoing interest in minimally invasive methods for sampling the airways. Collection of exhaled breath condensate (EBC), and analysis of exhaled breath using an electronic nose (eNose) are two methods which have significant potential. Our group is currently investigating the value of both exhaled breath condensate and the electronic nose for the evaluation of biomarkers in patients with a wide range of respiratory diseases including asthma, COPD, sarcoidosois and lung cancer. However, several challenges relating to specificity and sensitivity exist and further research is required.