Objective To study the effect of scan position consistency on computer tomography-magnetic resonance (CT-MR) images automatic registration in patients with nasopharyngeal carcinoma.Methods Fifteen patients with nasopharyngeal carcinoma were enrolled in this study and scanned with the same position to acquire CT images and MR-1 images. Then they were reacanned with different position for MR-2 images. Image registration of CT-MR-1 and CT-MR-2 was finished using mutual information method.The registration errors were evaluated by measuring the distances between marks. Results The error of au-tomatic CT-MR registration with consistent scan position was 1.32 nun, comparing with the minimum of 2.00 ram and the maximum of 3.83 mm with different positions. Conclusion Keeping consistent scan position can improve the accuracy of image registration.