Nowadays, managers tend to compare their organizations with the others as well they want to have benchmarks. Benchmarking should be based on correct updated organizational critical factors. Balanced scorecard (BSC) is the tool to translate the organizational strategic goals into the operational critical factors by its strategy map. It individually may not use as the tool for organizational comparison. Data envelopment analysis (DEA) is essentially used to evaluate decision making units (DMUs) from the best possible relative efficiency. But it's incapable of defining its input and output indexes efficiently. So, in this paper the most important strategic factors obtained from BSC are employed as the input data for DEA. This may lead us to a comprehensive benchmarking method to attain the reliable appropriate results for each organization in each period. Finally, the proposed method is practically tested and the results are illustrated in the following paragraphs.