[en] The individual resonant frequencies and the intercavity coupling constants of the cavities which comprise a side coupled linear accelerator chain show small deviations from the mean value, due to fabrication tolerances, and, in some cases, due to design. This paper makes use of a perturbation theory to predict the overall mode spectrum of the linear accelerator chain, given the measured values of the individual frequencies and the intercavity coupling constants. The predictions of the theory show good agreement with experimental measurements