Effects of perturbations of the whispering gallery modes (WGMs) in cylindrical microcavity resonators by embedded nano size particles are studied by the finite difference time domain modeling. Apart from the foreseeable effects of spectral shift and broadening of WGM resonances, we also observed a key feature of splitting of the WGM peaks. This splitting occurs as a result of formation of symmetric and antisymmetric standing waves inside the cavity. It is demonstrated that magnitude of the splitting reaches several angstroms for 5 μm cavities with index 1.59 supporting moderately high quality (Q≈10 5) WGMs. We show that this effect allows developing biomolecular sensors based on measuring this splitting in porous cavities or in cavities with liquid cores. ©2009 IEEE.