A quantum chemical simulation for radicals of a cation branch in irradiated L-a-alanine crystals was carried out. The large cluster approach was used for investigation of possible paths of radical transformation. Both intermolecular and intramolecular proton transfer together with decarboxylation process were considered. Relative total energies of various radical structures were obtained at the PM3 level followed by DFT calculation of hyperfine parameters for the protons of the corresponding radical. It was shown that in this crystal the radicals R2 and R3 observed by ESR and ENDOR techniques are the products of the transformation of the primary cation radical.