A new program for the molecular superposition of flexible molecules, IFMFIT (Improved or Interactive Flexible Molecular Fit), is presented. The essential new feature involves a complete revision of the representation of molecular structures making use of the briefly discussed Distance Matrix algorithm. A comparison is given between the input mode required by the original FMFIT program and that of our version as exemplified by the superposition of (R)‐chrysanthemic acid and (S)‐3‐methyl‐2‐(parachlorophenyl)‐butyric acid. This example demonstrates the superiority and the user‐interactive character made possible by our IFMFIT version. Copyright © 1986 John Wiley & Sons, Inc.