In this paper, electromagnetic wave scattering from a slightly rough interface inside a stratified medium is considered. A three-layer model for the medium is chosen, which allows us to investigate both possible cases of the medium's stratification: above and below the rough interface. It also is a simple but realistic model for the ground, in which the upper layer is thought to be vegetation or snow, while the middle layer and the homogeneous half-space below it represent the ground itself. The vegetation-ground interface is considered to be rough with statistically homogeneous corrugation, while the two other interfaces are flat. The backscatter coefficients for vertically and horizontally polarized waves are found in the framework of the small perturbation method combined with the Green function formalism. Such an approach allows one to consider arbitrary layers and, in this respect, go far beyond the radiative transfer theory. The influence of the stratification of the medium above and below the rough interface on the scattered field is analyzed numerically. Qualitatively new angular and frequency dependencies of backscattering are found. It is shown that in the case of small ohmic losses stratification of a medium can cause the deviation of backscattering up to 20 dB.