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In this paper, the problem of the stability of functionally graded thin plates with a microstructure is presented. To analyse this problem and take into consideration the effect of microstructure, tolerance modelling is used. The tolerance averaging technique allows us to replace the equation with non-continuous, tolerance-periodic, highly oscillating coefficients of the system of differential equations with slowly-varying coefficients, which describes also the effect of the microstructure. As an example, the buckling of a microstructur