In order to investigate the mechanism of the photochromic effect in yttrium oxy-hydride (YOxHy) thin films, Doppler broadening positron annihilation spectroscopy (PAS) was applied to probe the electronic structure and the presence of vacancies in YOxHy and related materials as a function of composition, UV illumination and thermal annealing. The Doppler S and W parameter depth profiles of a series of Y, yttrium di-hydride YH1.9+delta and Y2O3 thin films show strong systematic changes caused by the distinct differences in electronic structure of the metals Y, YH1.9+delta and the wide band gap insulator Y2O3. The Doppler broadening parameters of photochromic YOxHy (a semiconductor with a band gap of similar to 2.6 eV) are intermediate to those of YH1.9+delta and Y2O3. In order to probe the nanostructural changes related to the photochromic effect, the S parameter of YOxHy was monitored during in-situ UV illumination. A small but systematic increase of the S parameter was observed, possibly induced by generation of cation mono-vacancies or small vacancy clusters involving generated anion vacancies. The changes did not relax during bleaching under dark conditions, showing that the structural changes are not directly responsible for the photochromic mechanism. For temperatures above around 90 degrees C, thermal annealing leads to a substantial increase in the Doppler S parameter, pointing to the formation of vacancies by local removal of hydrogen. Simultaneously, the optical band gap increases, consistent with an increase in O:H ratios.