The transition radiation of a charged particle in a regular waveguide with periodically modulated anisotropic magnetodielectric medium during its passage perpendicular to the axis of the waveguide is considered. In a first approximation with respect to the small index of modulation the analytical expressions for the transverse-electric (TE) field and for the energy of transition radiation in the region of "weak" interaction between the field of radiation and the modulated filling are found. In particular, the case of a rectangular waveguide is considered. The analysis of obtained results shows, that the field in the waveguide represents the set of space harmonics with different amplitudes and in the expression for the energy loss of the particle appears member proportional to the small modulation index in the first degree.