We report the photoionization of ion beam desorbed amino acids using femtosecond laser pulses at 195 and 260 nm. Ionization of ion-desorbed glycine, alanine, valine, leucine, isoleucine, and phenylalanine using 195 nm laser pulses is found to produce almost exclusively a decarboxylated ion fragment, while tyrosine and tryptophan produce a functional group cation. The adiabatic ionization potentials for the former amino acids correspond to the removal of an electron from the amine nitrogen atom, while for tyrosine and tryptophan it corresponds to the removal of an electron from the aromatic functional group. We find that fragmentation is initiated by the formation of a radical site which leads to an alpha-cleavage reaction and, depending upon which electron is removed, results in the formation of a decarboxylated ion or a functional group ion. These results indicate that a significant fraction of the amino acids are desorbed intact, but are fragmented when ionized. Except for leucine, isoleucine, and phenylalanine, the mass spectra produced by 260 nm irradiation are similar to the mass spectra produced by 195 nm irradiation. When using these two wavelengths, the desorbed amino acids exhibit a 2- to 8-fold higher ion yield than is found using only secondary ions produced directly by the incident ion beam. Tyrosine exhibits up to a 40-fold increase in signal using 195 nm irradiation.