In the upcoming video coding standard, MPEG-4 AVC/JVT/H.264, motion estimation is allowed to use multiple references and multiple block sizes to improve the rate-distortion performance. However, full exhaustive search of all block sizes is computational intensive with complexity increasing linearly to the number of allowed reference frame and block size. In this paper, a novel search algorithm, Three Dimensional Predict Hexagon Search (3DPHS) is proposed. The 3DPHS patterns depend on the characteristics of motion vector distribution. It can predict the hexagon search pattern in horizontal or vertical direction. The proposed algorithm also considered the characteristics of multiple references and multiple block sizes in H.264. It can save all the same level search points for higher definition video sequences. The analysis shows that the speed improvement of 3DPHS over the Diamond Search (DS) and the Hexagon Based Search (HEXBS) is about 58% and 53% respectively.