We report on an experimental test of Babinet's principle in quantum reflection of an atom beam from diffraction gratings. The He beam is reflected and diffracted from a square-wave grating at near grazing-incidence conditions. According to Babinet's principle the diffraction peak intensities (except for the specular-reflected beam) are expected to be identical for any pair of gratings of complementary geometry. We observe conditions where Babinet's principle holds and also where it fails. Our data indicate breakdown conditions when either the incident or a diffracted beam propagates close to the grating surface. At these conditions, the incident or the diffracted He beam is strongly affected by the dispersive interaction between the atoms and the grating surface. Babinet's principle is also found to break down, when the complementary grating pair shows a large asymmetry in the strip widths. For very small strip widths, edge diffraction from half planes becomes dominant, whereas for the complementary wide strips the atom-surface interactions leads to a strong reduction of all non-specular diffraction peak intensities.