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In this paper, we plan the collision free motion for walking pattern generation of a humanoid robot. Our motion planner can take into account several features of the walking pattern generator. We first run the walking pattern generator by considering the contact wrench applied to the robot and monitor the collision among the links and the environments. Then, we plan the collision free motion for the period of time causing the collision. In our motion planner, we can consider the constraint condition which are the functions of time. Also, for keeping balance of the robot, we plan the motion with keeping the horizontal position of the COG as well as the position/orientation of the feet/hand. The effectiveness of the proposed method is confirmed by simulation and experiment.