Stability of organic photovoltaic cells is the key issue for their commercialization. Despite intensive investigations to clarify the causes of failure of devices, the process of degradation is not yet well understood. In this work, we made use of the trap measurements by the charge-based deep-level transient spectroscopy to study devices that have been aged by continuous exposure to artificial sunlight for 20 h, and we compared the trap parameters to those obtained in freshly prepared samples. With regard to poly (3-hexylthiophene) (P3HT)-based devices, the P3HT:phenyl C61 butyric acid methyl ester blend cells showed an additional deep trap level and a higher trap density. In the degraded devices, all the existing traps in the fresh sample were found, and there was no creation of additional defect levels. The density of several trap levels in the polymer was strongly reduced after aging. Analysis of the results suggests that a phase separation in the photoactive blend has occurred, leading to a better organization of the polymer domains to lower defect states.