A kilo-voltage cone-beam CT (CBCT) attached to a linear accelerator can verify a target position in each radiation therapy. If CBCT images can be used in dose calculation, we can verify an actual dose distribution on every treatment day. However, the CBCT images are degraded by several factors, and so we cannot use the CBCT images directly in place of conventional multi-slice CT (MSCT) images that are used in the initial dose planning. In this paper, we proposed a new method for using CBCT and MSCT images in the calculation of a dose distribution. Our proposed method segments the CBCT and MSCT images into regions of three major organs (lungs, bones and soft tissues) by use of histogram analysis. We also calculated a value such as the median of the MSCT numbers in each region of the MSCT images, and we set three representative values to the corresponding regions of the CBCT images. In the calculation of a dose distribution, we used these modified CBCT images. The validity of our method was confirmed with experiments in which we used images of a heterogeneous phantom and patients' lungs in comparison with conventional methods. The results showed that the dose distribution determined by our method was similar to that of the initial dose plan, and our method was superior to the conventional methods in terms of pass rates of a distance-to-agreement analysis and γ analysis. The results of a dose-volume-histogram analysis also showed the accuracy of our proposed method.