Rationale: much effort is being made to discover non-invasive biomarkers of chronic airways disease that might enable better management, predict prognosis and provide new therapeutic targets. Objectives: to undertake a comprehensive, unbiased proteomic analysis of induced sputum and identify novel non-invasive biomarkers for chronic obstructive pulmonary disease (COPD). Methods: Induced sputum was obtained from COPD patients with a spectrum of disease severity and control subjects. Two-dimensional gel electrophoresis and mass spectrometric identification of differentially expressed proteins was first applied to induced sputum from GOLD Stage 2 COPD patients and healthy smoker control subjects. Initial results thus obtained were validated by a combination of immunoassays (Western blotting and ELISA) applied to a large subject cohort. The biomarkers were localised to bronchial mucosa by immunohistochemistry. Measurements and main results: of 1325 individual protein spots identified, 37 were quantitatively and 3 qualitatively different between the two groups (p