Estimation of the direct operating cost (DOC), seat mile cost (SMC) and price of the aircraft, is an important aspect in commercial transport aircraft design. The operating costs are classified into two categories which are direct operating cost (DOC) and indirect operating cost (IOC). IOC is difficult to estimate well, since it depends on the services that the airline (customer) offered, and can vary considerably between operators. Therefore, DOC is useful and widely-used parameter for comparative analysis. Many methodologies have been developed to estimate DOC. There are three common methodologies that are in use in preliminary aircraft design. These models, namely the ATA, NASA and the AEA form the basis of cost estimation. In the preliminary aircraft design stage, cost estimates are required to evaluate the viability of the design being considered. This paper presents the cost estimation methodology of these three methods and compares the estimated costs for a range of current aircraft. The paper also presents a new empirical relationship for estimating the DOC.