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Radiation effects in cerium doped Gd3(Al,Ga)5:O12 (or GGAG) single crystals irradiated by swift heavy ions with fluences ranging from 6·1010 to 2·1012 ions/cm2 have been studied. A stable strong induced absorption observed in the spectral range 200–350 nm correlates with the irradiation fluence. It is suggested that several centers are responsible for this induced absorption in GGAG single crystals and their possible origin (F-type centers and V-centers or holes trapped near cation vacancies) is proposed and discussed. The swift heavy ions irradiation strongly modifies the luminescence properties of GGAG, namely, the excitation spectra of the Ce3+ emission, which have been measured over a wide spectral range including vacuum ultraviolet diapason. In particular, it was shown that the formation of the stable radiation defects under swift heavy ions irradiation leads to the effective Ce4+ → Ce3+ transformation in the Mg2+ co-doped GGAG single crystals. The reasons leading to the alteration in the luminescence properties of irradiated GGAG single crystals are elucidated and discussed.