Safe, fast, efficient and effective railway is a main factor of economic development level of every country. This paper uses the DEA method to evaluate and compare the efficiency of 12 Regions of RAI. In addition, we introduce the reference(s) unit(s) for every inefficient region, and determine the amount of input decrease and/or output increase need to become them efficient. Findings indicate that in 2006, 4 regions of 12 are in Constant Return to Scale (CRS) status and 7 of them in Variable Return to Scale (VRS), and the average efficiency is 0.730 and 0.888, respectively. In other words, RAI works 27 percent under its capacity. More over results indicate that Hormozgan, Khorasan, Tehran and Isfahan Regions have the most efficiency respectively. The results show that the 8 regions, have been working in Increaser Return to Scale and 4 reminder Regions in Decrease Return to Scale. According to this results, we submit the suitable suggestion for improve the efficiency of the inefficient regions.