Thermodynamic calculations of ion exchange for divalent cations were made for clinoptilolite in natural state and after irradiation with three different doses of β-radiation (1012, 1015 and 3 × 1016 e/cm2) and γ-radiation (70 Mrad). The samples were equilibrated with binary systems of divalent cations, namely Sr2+ ↔ 2Na+, Ca2+ ↔ 2Na+ and Mg2+ ↔ 2Na+ at 25 °C and total solution normality of 0.025 N. The selectivity order Sr2+ > Ca2+ > Mg2+ was observed in non-irradiated clinoptilolite. After irradiation with γ-radiation the affinity of clinoptilolite for Sr2+ increased and that for Mg2+ decreased, whereas the affinity for Ca2+ remained unchanged. Irradiation with β-radiation influences selectivity order and clinoptilolite affinity decreases for Sr2+, whereas it increases for Ca2+. For the sample irradiated with maximum dose of β-radiation the selectivity was almost identical for Ca2+ and Sr2+. The crystallographic parameters and exchangeable cation site coordinates were refined for all samples with the Rietveld method. The structure refinement of Sr2+-saturated samples yielded changes both in exchangeable sites and site occupancy in channels A and B after irradiation with β-and γ-radiation. The cation sites Sr1 and Sr3 exhibit major changes both in site coordinates and site occupancy after irradiation with β-radiation. In addition, irradiation with γ-radiation yielded major changes in Sr1 occupancy, whereas coordinates changed only slightly. These structural modifications control the observed changes in thermodynamic parameters after irradiation.