Structural characterization of folding intermediates has been one of the important steps toward understanding the mechanism of protein folding. However, it has been very difficult to obtain high-resolution structures of folding intermediates. Such results have become available only very recently. Here, we review a procedure that uses the native-state amide hydrogen exchange-directed protein engineering method to populate partially unfolded intermediates and multidimensional NMR to solve the high-resolution structures of the intermediates.