In the present work, excimer laser irradiation below the ablation threshold is successfully applied as a tool for surface modification of vapor grown amorphous zirconia (ZrO2) thin films. Characterization of virgin and laser processed areas was performed by optical spectroscopy, transmission electron microscopy (TEM), selected area electron diffraction (SAED), low angle X-ray diffraction (LAXRD) and reflection high energy electron diffraction (RHEED). The occurrence of phase transitions to orthorhombic or monoclinic modification of amorphous zirconia on laser parameters dependency is established. Separation of a new Zr phase is detected in parallel to the formation of crystalline zirconia phases. The observed structure transformations strikingly coincide with some polymorphic transitions in zirconia powders and sintered ceramics. The results obtained demonstrate the necessity for applying both surface and in-depth analytical techniques in characterizing excimer laser induced changes in thin ZrO2 films.