The utilization of inverted structures in organic solar cells (OSCs) has been demonstrated to provide higher efficiency and stability as compared to standard structure devices. The improvement of the cell performance is thought to be linked to the electron and hole transporting layers (ETL and HTL), which also play key role in preventing the cell from extrinsic degradation. However, from the defect point of view, the presence of these layers can introduce new sources of charge carrier trapping, and therefore can impact on the long term stability and electrical property of the solar cells. In this work, we report results on investigations of defects in inverted solar cells using blends of poly(hexylthiophene) (P3HT) and 6,6-phenyl-C61-butyric acid methyl ester (PCBM) as the absorbing layer, while zinc oxide (ZnO) was used as the ETL. The defects in devices were determined by the charge based deep level spectroscopy (Q-DLTS). The results indicated new defect states in inverted OSCs as compared to the standard P3HT:PCBM device. Defects of energy in the range of 10–470 meV have been determined by the charge peak corresponding to the high relaxation time domain, assigning to the heterojunction bulk of the cells. Additional traps observed through the onset of a charge peak in the low relaxation time domain have a low energy level and are assigned to interface defects. These defects are supposed to originate from the zinc oxide contact and may affect the stability of the solar cells in operation.