In this paper we study the effect of molecular orientation on the observed Raman spectra in waveguide Raman spectroscopy. Depolarization ratios differ from those in 'normal' Raman spectroscopy due to the polarization properties of the guiding modes that excite the Raman scattering. Waveguide Raman spectra of submonolayers of cytochrome c and NiOEP were recorded using different polarization settings. The observed depolarization ratios strongly deviate from those obtained in bulk Raman spectra. Using the derived equations for the depolarization ratios, the preferred orientation angle of the molecules can be obtained from the observed depolarization ratios. From these results we first conclude that high-quality spectra of sub-monolayers can be obtained using waveguide Raman spectroscopy and secondly, that these spectra can be used to determine the preferred orientation of the molecule with respect to the waveguide surface.