Thermodynamic calculations of ion-exchange reactions were applied for clinoptilolite in a natural state and after irradiation with three doses of β-radiation (1012, 1015, 3 × 1016 e/cm2) and γ-radiation (70 Mrad). Samples were equilibrated with binary systems of K+ ↔ Na+ and Cs+ ↔ Na+ at 25° and a total normality of 0.025 N. Selectivity for K was not affected after γ-radiation with doses of 1012 and 1015 e/cm2 (ΔG° = −6.37 kJ/equiv, lnKα = 2.58 for the original clinoptilolite), whereas it increased considerably after 70 Mrad of γ-radiation (ΔG° = −7.88 kJ/equiv, lnKα = 3.18). Selectivity for Cs+ increased for the clinoptilolite irradiated with β-radiation (1012, 1015, 3 × 1016 e/cm2) and γ-radiation (70 Mrad). ΔG° and lnKα for original sample and Cs+ ↔ Na+ were −7.33 kJ/equiv and 2.96, respectively. Irradiated samples with β-radiation 1012, 1015, 3 × 1016 e/cm2 and 70 Mrad γ-radiation yielded ΔG° and lnKα −7.41, −8.83, −8.60, −8.25 kJ/equiv and 2.99, 3.57, 3.47, 3.33 for Cs+ ↔ Na+, respectively. Remarkable amorphization of clinoptilolite was observed after exposure at the highest dose of β-radiation (3 × 1016 e/cm2) with a concomitant decrease in cation-exchange capacity (CEC). Crystallographic parameters and especially exchangeable cation site coordinates were refined for all samples with the Rietveld method. Cesium-saturated samples exhibited changes in the cation sites Cs2 and Cs3, which are next to clinoptilolite channel walls with lower Al3+ for Si4+ substitution. The observed changes include a shift in cation sites Cs2 and Cs3 toward channel walls and occupancy decrease in site Cs2.