We report on a joint morphological/photoelectrical study of polymer-based photovoltaic (PV) cells in working conditions. The bulk heterojunction devices investigated are based on an active layer of poly(3-hexyl thiophene) blended with methano-fullerene, combining good PV performances with promising stability. The set-up adopted allowed the electrical properties of the device to be directly correlated to the modification of the electrode morphological parameters (thickness and roughness), which were obtained by in situ energy dispersive X-ray reflectometry (EDXR). The results of this joint time-dependent characterization demonstrated how the observed photo-induced oxidation process, limited to the buried electrode interface, is responsible for a fast decrease in the photo-current. The time-resolved measurements allowed to rule out the dynamics of the morphological changes and showed that the interface morphology may be stabilized by annealing treatments, with a significant improvement of the cell efficiency. (c) 2008 Elsevier B.V. All rights reserved.