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The fluorinated organic solvents 1,1,1,3,3,3-hexafluoro-2-propanol (HFIP) and hexafluoroacetone trihydrate (HFA) have been successfully used to produce silk fibroin fibers with high strength. To understand the reasons for the difference in strength between regenerated silk fibers prepared from these two solvents, we analyzed and compared properties of the native silk fibroin and (AGSGAG)2, a model for the crystalline part of fibroin, in the two solvents. The 13C and 1H chemical shifts obtained from 1H−13C HSQC spectra of silk fibroin in HFIP, HFA, and water indicates that silk fibroin formed helix-like structure in the fluorinated alcohols. A similar tendency was observed for (AGSGAG)2 although the chemical shift change is smaller. Intramolecular 1H−1H NOE data for (AGSGAG)2 imply the presence of helical structures in the middle part of the peptide in HFIP and but not in HFA, although an equilibrating collection of conformations likely are present in both solvents. For the peptide dissolved in HFIP, cross...