Trefoil factors (TFFs) 1, 2 and 3 are small polypeptides that are co-secreted with mucin throughout the body. They are up-regulated in cancer and inflammatory processes in the gastrointestinal system, where they are proposed to be involved in tissue regeneration, proliferation and protection. Our aim was to explore their presence in pulmonary secretions and to investigate whether they are up-regulated in pulmonary diseases characterized by mucin hypersecretion. Bronchioalveolar lavage fluid was obtained from 92 individuals referred to bronchoscopy. The patients were grouped according to diagnosis and pulmonary function. The concentrations of TFF1, TFF2 and TFF3 were measured by ELISA. All three peptides were detected in bronchioalveolar lavage fluid. Patients with chronic obstructive pulmonary disease had concentrations two to three times above the levels in the healthy reference group, and patients with pulmonary malignancies had concentrations of TFF1 and TFF2 three times that of the reference group. The results suggest that TFFs are involved in tissue regeneration, proliferation and protection in lung diseases.