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A new analytical formalism to study the effect of discontinuities in a nonreciprocal waveguide has been developed. The analysis is based on 1) the general orthogonality relation obtained from the reciprocity theorem, 2) the modal expansion of the transverse electromagnetic fields within the waveguide, and 3) the continuity of the tangential components of such electromagnetic fields at both sides of the discontinuity. The formalism is presented in a matrix form, which allows the treatment of several discontinuities as a simple summation and product of coupling and propagation matrices. The matrix formalism is developed for magnetooptic waveguides in the three different orientations of the magnetization, and, within this context, two practical applications of magnetooptic isolators are studied.