Characterizing the structure properties of unfolded proteins is important for understanding the stability and folding of native proteins. However, little structural information is available for the unfolded state. Using recently developed heteronuclear multi-dimensional NMR techniques, the 1H, 13C and 15N chemical shift assignments of the FK506 binding protein (FKBP) unfolded in concentrated urea and guanidine hydrochloride (GuHCl) solutions have been obtained, and the structural properties of unfolded FKBP have been characterized. FKBP displays extensive conformational averaging when unfolded in urea and GuHCl, but defined regions of secondary structure are present. Subtle differences regarding the location and stability of the secondary structures exist between the two solvents. Secondary structure formation in unfolded FKPB was correlated with statistical and thermodynamic predictions of helix formation as well as with the three-dimensional structure of folded FKBP determined by NMR and X-ray crystallography. Residues involved in secondary structures in unfolded FKBP are generally found in the same type of secondary structure in the folded protein. An exception to this was found at the C terminus of FKBP, which forms a different secondary structure in the unfolded and folded states.