This paper presents a three-dimensional (3-D) volume registration method that uses 3-D phase correlation to estimate the respiration-induced tumor motion in four-dimensional (4-D) thorax computed tomography (CT) for radiation therapy. The proposed method is an extension of 2-D phase correlation method to 3-D volume registration. Given two CT volumes obtained from different respiration stages, the tumor motion is modeled as a translational shift between the volumes. The 3-D phase correlation is obtained from the 3-D inverse Fourier transform of a normalized cross power spectrum of the volumes. The tumor motion along three directions is estimated by locating the highest peak in the 3-D phase correlation. In order to improve the estimation accuracy, we extend the 3-D phase correlation to sub-voxel accuracy. Experimental results demonstrate the effectiveness of the proposed method relative to a conventional 2-D phase correlation-based method.