A coupled integral equation formulation of analysing a generalised multilayer frequency selective surface is described. An iterative spectral technique has been adopted for the calculation of the induced currents, aperture fields and the plane wave transmission coefficient. In this scheme, the error is minimised using variational expressions for the element current in each of the unit cell areas of the multilayer structure. The effect of the distance separating the arrays and state of incidence to the rate of convergence and the transmission coefficient is discussed. The analysis described in the paper is not restricted to identical element geometries.