Irradiation of lithium niobate crystals with $41\mathrm{MeV}$ ${}^3\mathrm{He}$ ions causes strong changes of the ordinary and extraordinary refractive indexes. We present a detailed study of this effect. Small fluence of irradiation already yields refractive index changes about $5\times {10}^{-4}$ ; the highest values reach $3\times {10}^{-3}$ . These index modulations are stable up to $100°\mathrm{C}$ and can be erased thermally, for which temperatures up to $500°\mathrm{C}$ are required. A direct correlation between the refractive index changes and the produced lattice vacancies is found.