A wide variety of biomarkers have been associated with asthma and chronic obstructive pulmonary disease (COPD) and examined as therapeutic targets in these diseases. Biomarkers examined in asthma and COPD range from small, pro-oxidant compounds and exhaled gases to proteins and cytokines and have great promise as aids in differential diagnosis, predictors of risk and outcome and in understanding the pathophysiology of disease. Biomarkers have been measured in numerous sites, including blood, induced sputum and bronchoscopy samples. Biomarkers measured in exhaled breath are particularly exciting as they are completely noninvasive. However, no single biomarker can encapsulate the entirety of inflammatory events and structural changes which occur in the airways in asthma and COPD. This is likely why no single biomarker has been shown to correlate consistently with traditional outcomes, such as pulmonary function or symptoms, or to accurately measure or predict the response of patients to anti-inflammatory drugs. In addition, the methodology for collecting and measuring most biomarkers in clinical specimens has not been standardized and there are significant problems with reproducibility. Many techniques are time-consuming and require specialized skills and expensive equipment or involve risk to the patient. Despite this, the study of biomarkers in respiratory diseases is growing rapidly. For now, they remain research tools although they retain significant promise for increasing our understanding of these diseases and one day having a role in management. This review will examine the current state of knowledge on the potential of biomarkers in serum, exhaled breath, sputum, bronchial biopsies and bronchoalveolar lavage to be diagnostic tests and outcome measures in COPD and asthma.