It has been found that patterns acid inhomogeneities on the surface of the waveguide used fur optical waveguide lightmode spectroscopy applications can produce broadening and fine structure in the incoupled light peak spectra. During cell spreading on the waveguide, a broadening of the incoupling peaks is observed, while regular microstructures on the incoupling grating produce shifts and splitting of the peaks. A theoretical model, based on the zigzag wave representation of light propagation in a planar optical waveguide has been developed in order to understand the physical background of the observed effects. Numerical results are given for the different cases observed, and they are compared with the experimental data. Several possible applications of these effects are considered.