Background: Abnormalities of the intracellular metabolism of the hydrophobic surfactant proteins SP-B and SP-C and their precursors may be causally linked to chronic childhood diffuse lung diseases. The profile of these proteins in the alveolar space is unknown in such subjects. Methods: We analyzed bronchoalveolar lavage fluid by Western blotting for SP-B, SP- C and their proforms in children with pulmonary alveolar proteinosis ( PAP, n = 15), children with no SP- B ( n = 6), children with chronic respiratory distress of unknown cause ( cRD, n = 7), in comparison to children without lung disease ( n = 15) or chronic obstructive bronchitis ( n = 19). Results: Pro-SP-B of 25 - 26 kD was commonly abundant in all groups of subjects, suggesting that their presence is not of diagnostic value for processing defects. In contrast, pro-SP-B peptides cleaved off during intracellular processing of SP- B and smaller than 19 - 21 kD, were exclusively found in PAP and cRD. In 4 of 6 children with no SP- B, mutations of SFTPB or SPTPC genes were found. Pro-SP-C forms were identified at very low frequency. Their presence was clearly, but not exclusively associated with mutations of the SFTPB and SPTPC genes, impeding their usage as candidates for diagnostic screening. Conclusion: Immuno-analysis of the hydrophobic surfactant proteins and their precursor forms in bronchoalveolar lavage is minimally invasive and can give valuable clues for the involvement of processing abnormalities in pediatric pulmonary disorders.