This paper deals with stage optimization of anti-air missiles. Conceptually, stage optimization is a two-loop optimization problem for which the inner loop determines control inputs for the optimal trajectory while the outer loop minimizes the stage weights. In practice, the optimal control inputs are replaced by guidance commands produced by practical guidance laws, resulting in some degradation of the system performance. In this paper, stage optimization considering practical guidance laws for the launch and mid-course guidance phases is proposed to precisely investigate the effect of guidance laws on the stage weights required for the mission. Guidance parameters, virtual target positions, coasting time, and the stage weights are defined as the objective parameters of stage optimization, and the co-evolutionary optimization method is used to find the optimal solution. Applying the proposed method to the stage optimization of a realistic anti-air missile system demonstrates that the missile system needs an extra weight of 4-6 kg compared to the classical two-loop optimization, to meet the same system requirements.