The structure of hydrophobic pulmonary surfactant-associated proteins SP-B and SP-C have been studied in different acetonitrile (ACN)/water and trifluorethanol (TFE)/water mixtures by circular dichroism and fluorescence spectroscopy to analyze the conformational flexibility of these proteins in response to changes in solvent composition. SP-B presented a very stable conformation in all the assayed ACN/water mixtures and in TFE/water mixtures containing until 70% TFE, showing around 40% alpha-helix. When SP-B was transferred to mixtures containing more than 70% TFE, the percent of alpha-helix in SP-B increased up to 60%. The fluorescence emission spectra of SP-B in the different solvents showed that tryptophan residues are more sensitive to solvent changes than those of tyrosine, reflecting differential effects on different protein microenvironments. The effect of solvent changes on the two tryptophan populations detected by fluorescence spectra was also different. A model for the folding of SP-B dimers, dominated by intra- and intermolecular disulphide bonds, is proposed. Surfactant protein SP-C revealed a secondary structure much more sensitive to solvent composition than SP-B. It had a main alpha-helical conformation in ACN/water solvents which was up to 63% in mixtures containing more than 60% ACN. When the protein was transferred to solvents containing less than 60% ACN, its secondary structure possessed less percent of alpha-helix and an increased percent of beta-structure. On the other hand, SP-C had a main beta-sheet secondary structure in all the assayed TFE/water mixtures, with 30-40% alpha-helix and around 50% beta-structure. The strong dependence of SP-C conformation on the nature of the solvent is interpreted to arise from its high hydrophobicity and the possible occurrence of protein-protein interactions.