This study presents the experimental and numerical assessment of natural frequencies and corresponding mode shapes of cross-laminated timber (CLT) beams subjected to a series of damage cases. To this aim, two different cantilever CLT beams consisting of three layers are considered. Damages on the beam are represented by transversal notches (cracks) through the thickness. Six damage scenarios on the beam models are considered. Experimental measurements via the operational modal analysis are performed to extract the natural frequencies and corresponding modes shapes of the beams under the considered damage cases. To verify the experimental results, the finite element modal analysis is also performed by ANSYS(R) finite element software. The material moduli necessary for the numerical analyses are determined from a single-layer cantilevered timber beam by applying the finite element model updating procedure. The effect of damages (cracks) on the modal characteristics of CLT beams is investigated. Experimental and numerical results show that especially the cracks near the fixed-end are highly effective on the natural frequencies, corresponding mode shapes, and damping ratios of the beams considered. In cases of multiple damages, the serious damage severity causes a change in the order of mode shapes. There is not found a direct relationship between the gluing applied to the piecewise material in the core layer and the modal characteristics. The results from this study can highly benefit the emerging research field of structural health monitoring on timber structures.