Radiation treatment requires a precise procedure for Intel-fraction repositioning of the patient. The purpose of this study was to determine the accuracy of our fixation device in treatment position and to evaluate the setup accuracy with two different methods. The positioning data of 19 canine patients with tumors in the head region (oral, nasal, cerebral) treated with photon or proton irradiation were included in this study. The patients were immobilized by means of an individualized fixation device. Focus was set upon interfraction displacement with systematic and random components. In one method, treatment position was evaluated using single plane port radiographs and megavoltage x-rays. In the other method, two orthogonal CT-topograms were acquired to evaluate the precision of positioning of the patient in the immobilization device. Systematic and random displacements were calculated and presented as mean values with corresponding 95% confidence intervals. In spite of a difference between both methods, the positioning seemed to be accurate within the expected range. It seems that a safety margin of 3.7 mm would be enough for both methods to take into account systematic and random position variability in the fixation device, thereby preventing geometric inaccuracies of treatment delivery. The reported immobilization protocol provides accurate patient immobilization for photon and conformal proton radiation therapy.