Biomarkers with potential utility in the diagnosis and prognosis of asthma and chronic obstructive pulmonary disease (COPD), and in monitoring the natural history of these diseases and the effect of therapeutic interventions, are being widely researched. This review critically describes the methodologies used for obtaining and analysing appropriate biofluid, tissue and exhaled breath samples for biomarker analysis. Currently measurements of sputum eosinophils and exhaled nitric oxide in asthmatics are the best established markers for disease activity and response to anti-inflammatory therapy. Circulating C-reactive protein (CRP) levels have been shown to predict risk of hospitalisation and death from COPD. Biomarker measurements in exhaled breath condensate are the least well-validated techniques. Other assessments in both conditions have potential value in clinical use but require further research and validation.