Data Envelopment Analysis (DEA) has been one of the most important tools on measuring the relative efficiency of different similar units such as transportation systems using terminals, airports, etc. In this study, we perform an empirical analysis on Iranian airports based on DEA methods to measure the efficiencies of various airports. One of the primary issues on many traditional DEA methods is that the data are almost always contaminated with noise. We use a DEA method which could handle the uncertainty associated with input and output data. The results of this comprehensive study show that most of the active airlines are practically inefficient and the government could significantly increase the efficiencies of the airports by setting new regulations and rules.