A fast integral equation based method has been developed for the analysis of the scattering by multiple dielectric posts in a rectangular waveguide. Each post may have a single or multiple inclusions. Each inclusion has cylindrical shape. Cylindrical inclusions may be metallic and/or dielectric. The numerical results are in good agreement with those computed using Ansys HFSS that employs the finite element method. The comparison of CPU time of the two methods showed that the developed method solves the same problem several orders of magnitude faster than HFSS. The method allows one to make measurements of complex dielectric constant and perform filter optimization process much faster.