Mutual information(MI)-based image registration is effective in registering medical images, but it is computationally expensive. This paper accelerates MI-based image registration by dividing computation of mutual information into spatial transformation and histogram-based calculation, and performing 3D spatial transformation and trilinear interpolation on graphic processing unit(GPU). The 3D floating image is downloaded to GPU as flat 3D texture, and then fetched and interpolated for each new voxel location in fragment shader. The transformed re-sults are rendered to textures by using frame buffer object(FBO)extension, and then read to the main memory used for the remaining computation on CPU. Experimental results show that GPU-accelerated method can achieve speedup about an order of magnitude with better registration result compared with the software implementation on a single-core CPU.