Infrared multiple photon dissociation (IRMPD) spectroscopy is a very powerful technique to characterize the structures of ions and ionic clusters. The structures of Gly and Pro proton-bound homodimers have been investigated using this method in combination with theoretical calculations. For the protonated Gly dimer, a new most stable isomer, GG-CS01, has been experimentally confirmed to be the dominant species. Direct IR spectroscopic evidence indicates that zwitterionic proline exists in the protonated proline dimer in the gas phase. This zwitterionic isomer (PP-ZW01) is the dominant species, and the most stable nonzwitterionic isomer (PP-CS01) also coexists under the experimental conditions.