In this paper, a three-dimensional transient inverse heat conduction (IHC) procedure is presented to estimate the unknown boundary heat flux of thick functionally graded (FG) plates. For this purpose, the conjugate gradient method (CGM) in conjunction with adjoint problem is used. A recently developed three-dimensional efficient hybrid method is employed to solve variable-coefficient initial-boundary-value differential equations of direct problem as a part of the inverse solution. The accuracy of the inverse analysis is examined by simulating the exact and noisy data for problems with different types of boundary conditions and material properties. In addition to rectangular domain, skew plates are considered. The results obtained show good accuracy for the estimation of boundary heat fluxes. (c) 2008 Elsevier Ltd. All rights reserved.