Conceptual and preliminary designs of future aircraft have become increasingly complex due to the enlargement of the basic criteria for evaluating emerging solutions. In the past, the basic performance characteristics of an airplane were the only selection criteria. Today, more and more emphasis is placed on factors such as impact on the environment, cost-effectiveness, or comfort of travel. The method for optimization of the key parameters of a small aircraft for use in the initial phase of a project is presented in this paper. It takes into account the requirements of aviation safety imposed by the European Union certification specifications CS-23 and requirements of aircraft competitiveness. Requirements and design assumptions were formulated based on the concept of the Small Air Transport system (SATs). The method is based on the multidisciplinary design optimization and covers the basic areas related to the design of aircraft: aerodynamics, aircraft structure, performance and expected operating costs. The objective function is defined as the value of the direct operating cost per passenger-kilometre. An evolutionary algorithm was applied to solve the optimization problem. As an example of the use of this method, the optimization of design parameters of the two classes of aircraft, 9-seater and 19-seater was carried out. The results were compared with the parameters of aircraft, which are in service. Sensitivity analysis of the objective function with respect to selected parameters of the aircraft was also made. The analysis allowed to select the most important parameters responsible for the operational costs.