The stresses of transportation, weaning and commingling are associated with an increased incidence of bacterial and viral pneumonia in cattle. Proteins expressed in the epithelial lining fluid (ELF) of the lungs, in conjunction with resident leukocytes, represent the first line of defence against opportunistic pathogens, and stress-induced alterations in their expression may reveal markers of disease susceptibility. Bronchoalveolar lavage fluid was sampled in weaned and transported calves and ELF protein expression was compared to a control group of calves using two-dimensional electrophoresis (2DE). Serum and pulmonary haptoglobin were increased following stress concurrent with the number of blood neutrophils. Using 2DE, significant changes in expression were observed in spots identified by mass spectrometry as annexin A1 and A5, odorant-binding protein (OBP), isocitrate dehydrogenase, fibrinogen, heme-binding protein, alpha-2-HS-glycoprotein, alpha-1-antichymotrypsin and albumin. Quantification of OBP mRNA by real-time RT-PCR and OBP protein by western blot revealed gender-dependent differences in relative OBP expression in response to stress. These findings reveal stress-associated protein changes in pulmonary ELF and suggest a mechanism through which stress alters respiratory disease susceptibility.