Abstract <p>A mathematical model and a numerical method are proposed for solving Maxwell’s equations in structures with inhomogeneous waveguide ports based on a system of combined field integral equations. The model supports both perfect electric conductors and dielectric regions of arbitrary shape. In contrast to approaches requiring a special basis of the port’s eigenmodes, the proposed method allows the use of standard basis functions for currents (RWG and higher-order functions). This enables correct accounting of complex port cross-sections with various dielectrics and allows for seamless integration of such ports calculation into existing software packages for solving diffraction problems without modifying their core (including fast algorithms, e.g., MLFMM). The possibility of using second-order basis functions to achieve higher accuracy in S-parameter calculation is illustrated on model problems. Verification of the method was performed using examples of a waveguide with inhomogeneous dielectric filling and a horn antenna, showing good agreement with calculations in commercial software packages (HFSS, CST, FEKO) and with experimental data.</p>