We report an accurate and efficient full dimensional semiclassical ab initio method for calculation of energy level splitting due to tunneling in polyatomic system. The method is applied to 21-dimensional 9-atomic malonaldehyde molecule. The tunneling splittings obtained are DeltaE(H) 521.2 cm(-1) for hydrogen atom transfer and DeltaE(D) 53.0 cm(-1) for deuterium atom transfer, which are in excellent agreement with the experimental values of 21.6 cm(-1) and, 2.9 cm(-1) respectively. We believe that the present analysis gives the final solution to the longstanding problem. (C) 2003 American Institute of Physics.