Recent crystallography and diffraction studies of membrane proteins have revealed that the structure of specific medium loop segments between transmembrane helices fold back into membrane positions and play an important role in membrane protein folding and biological function. However, previous structure prediction methods of membrane proteins have not classified the type of loop segments. We have developed a new method for classification and prediction system of the specific medium loop segments in membrane proteins from amino acid sequence. To classify the loop segments, multi discriminant analysis with three factors, loop length, average hydrophobicity and intensity of amphiphilicity, was used.