Analysis of the in-plane free vibration of the circular and annular functionally graded disks by a meshfree boundary-domain integral equation method are presented in this paper. The material properties of the disks are assumed to grade in the radial direction obeying an exponential law. Based on the two-dimensional linear elastic theory, the motion equations of the FG disks are derived by using the static fundamental solutions, radial integration method as an efficient tool is adopted to treat the domain integrals which raised due to the material inhomogeneous and inertial effects. The natural frequencies and associate mode shapes are calculated for the FG disks with combinations of free and clamped boundary conditions. Parametric studies are also conducted to study the effects of the material gradients, radius ratios and boundary conditions on the frequency of the FG disks.