Zn-exchanged natural clinoptilolite was studied by powder X-ray diffraction and positron annihilation lifetime spectroscopy. The original clinoptilolite tuff was subjected to size fractionation by sedimentation and dissolution of cristobalite (opal-C). After Zn2+-exchange the purified clinoptilolite sample contained 2.2 Zn2+ ions per unit cell. Structural details obtained by Rietveld refinement showed that the Zn2+ cations are located in three sites (Zn1, Zn2 and Zn3) in the channels of the clinoptilolite. Site Zn1 is located in the centre of channel-A (Mg2+-M4 site). Site Zn2 is in channel-B, next to the calcium M2 position. A new Zn3 site is located in channel-A, in imminent proximity to Zn1. Positron Annihilation Lifetime Spectroscopy (PALS) was employed to assess the Zn exchange. As the cation content influences the free volume of the channels, the ion-exchange process can be monitored by PALS. The results suggest the existence of two sizes of cavities, in accordance with the structural refinement.