In Japan, a 5 year R&D project has been in progress toward the development of an environmentally friendly high performance small jet aircraft under auspice from NEDO (New Energy Development Organization) since 2003, in which new technical features have been investigated including advanced aerodynamics, new materials, and human centered cockpit. In this paper, we focus on aerodynamics and Multi-Disciplinary Optimization (MDO) R&D activities and applications to actual design phase. The MDO among aerodynamics, structures, and aeroelasticity of the wing of a small jet aircraft was performed using high-fidelity evaluation models. The objective functions were minimizations of a block fuel and the maximum takeoff weight. As a result, several non-dominated solutions were obtained and one solution was found to have one percent improvement in the block fuel. However, through the study, we found there still remain some concerns to obtain "practically enough" optimized solution. These concerns are such as airfoil shape representation, definition of design space, efficiency of the evaluation, etc. Several investigations to overcome these concerns are also presented in this paper. On the other hand, we have been developing the detail aerodynamic optimization modules simultaneously. These are engine-airframe integration and 2D high lift device design using unstructured adjoint method. We introduce overview of these modules and the whole design process utilizing the systems with these modules.