The purpose of this study was to clinically evaluate the automatic outline extraction properties using general-purpose deformable image registration (DIR) software for the head and neck region. To this end, we evaluated the following: (1) the difference between manual outline extraction carried out by a radiation therapy specialist and automatic outline extraction using the DIR software, and (2) the precision of the automatic outline extraction for the diachronic figure change and change in the organ shape. The manually-extracted outline and that extracted using the DIR software closely resembled each other at 0.70. Further, in the same case, the automatic outline extraction precision of the DIR software was greater at about 0.80. Our findings suggest DIR software to be useful for lessening the work involved in outline extraction.