New boundary integral equations are proposed for two-port slab waveguides which satisfy single mode condition. The boundary integral equations are combined with the orthogonality of guided mode and non-guided field. They are solved by the standard boundary element method with no use of mode expansion technique. Reflection and transmission coefficients of guided mode are directly determined by the boundary element method. To validate the proposed method, step waveguides for TE wave incidence and triangular rib waveguides for TM wave incidence are investigated by numerical calculations.