When we render 3D sound images using headphones or speakers, the main key of this technology is the Head-related transfer function (HRTF) database. Even though there are various HRTF databases, they have some drawbacks such as detrimental effects caused by imperfect measuring environment and insufficient measurement points. Moreover there is no database with Korean subjects. We are planning to develop the HRTF database for Korean. As a first step to establish the HRTF database aimed at Korean, the new HRTF measurement system with minimized aforementioned drawbacks is designed. In this paper, the newly designed HRTF measurement system is introduced and the overall effects caused by the diffraction of the apparatus, especially the headrest and backrest of the chair, are analyzed. The backrest of the chair does not distort the HRTFs significantly while the headrest makes significant distortion on the HRTFs and it could have significant effects on directional perception. We determined acceptable head rotation angle and head position of the subject for accurate HRTF measurement based on the experiments with B&K HATS. We conclude that the 3 degrees of the head rotation and the 1.5cm front/back/left/right shift of the head do not distort the HRTFs significantly.