The proton affinities of proline, cis-3-methylproline and cis-3-ethylproline have been measured by the kinetic method using an ion trap instrument; the values obtained are 936, 940.5, and 943 kJ mol(-1), respectively. The experimental values are consistent with those obtained by high-level ab initio calculations (B3LYP/6-31+G*//B3LYP/6-31G* and B3P86/6-31+G*//B3LYP/6-31G*). Several conformations of neutral and protonated proline were considered, in particular the endo and exo ring structure and the position of the carboxyl group. These results show the importance of the position of the hydrogen atom of the carboxyl group in determining the most stable protonated proline structure. Copyright (C) 2003 John Wiley Sons, Ltd.