In the present work, a three-dimensional (3D) elastic plate model capturing the small scale effects is developed for the free vibration of functionally graded (FG) nanoplates resting on elastic foundations. The theoretical model is formulated employing the nonlocal differential constitutive relations of Eringen in conjunction with the 3D equations of motion of elasticity.The material properties are assumed to vary continuously along the thickness of the nanoplate in accordance with the power law formulation. Through extending the generalized differential quadrature (GDQ) method to the three-dimensional case, the governing equations are simultaneously discretized in every three coordinate directions and are then recast to the standard form of an eigen value problem. Solving the acquired problem, the natural frequencies of the nanoplates with different boundary conditions are calculated. The convergence behavior of the numerical results is checked out and comparison studies are conducted to make sure of the accuracy and reliability of the present model. Finally, the dependence of the vibration behavior of the nanoplate on edge conditions, elastic coefficients of the foundation, scale coefficient, mode number, material and geometric parameters are discussed.