Exhaled breath condensate (EBC) may be an attractive noninvasive alternative to bronchoscopy, bronchoalveolar lavage and induced sputum for diagnosis and monitoring of pulmonary disease. The aim of the present study was to identify proteins in EBC by mass spectrometry. Protein in EBC was characterised by gel electrophoresis of freeze-dried EBC samples, and individual proteins were identified by mass spectrometry. Saliva, ambient air condensate (AAC) and EBC were collected from normal human volunteers with or without a filter to remove particles from air. In some instances, EBC was condensed by breathing compressed air. Samples were freeze-dried and analysed by SDS-PAGE and peptide mass fingerprinting. Three major bands were seen in EBC and AAC, and were identified by peptide mass fingerprinting. The probability-based Mowse score was significant only for cytokeratin (CK) 1, CK2 and CK10. In the catalogue of human cytokeratins, CK1, CK2, CK9 and CK10 are described in keratinising epidermis. Saliva did not contain keratin and compressed air EBC contained markedly less keratin. Filtration of inspired air did not remove contaminating keratin. In conclusion, skin keratin in exhaled breath condensate derives from ambient air and not from the respiratory tract.