The effects of perturbations of whispering gallery modes (WGMs) in cylindrical microcavities by embedded particles are studied by FDTD modeling. The principal effects are: i) spectral shift of the WGM-related peaks caused by the variation of the average index, ii) broadening of the WGM peaks introduced by the scattering, and iii) splitting of the WGM peaks due to formation of symmetric (SSW) and antisymmetric (ASW) standing waves. The focus of this work is on the last effect. We show that it can be maximized by placing the nanoparticle inside the cavity at a position corresponding to the antinode of the radial distribution of intensity of WGM. It is demonstrated that in this case the magnitude of splitting reaches several angstroms for 5 μm cavities with index 1.59 supporting moderately high quality (Q≈105) WGMs. We show that for relatively small particles with radius <70 nm and index contrasts <0.2 the magnitude of SSW/ASW splitting is linearly dependent on the size and index of the nanoparticle. This allows developing biomolecular sensors based on measuring this splitting in porous cavities. It is predicted that a similar effect of splitting can occur in semiconductor microdisks and pillars where the role of embedded dielectric nanoparticles can be played by self-assembled quantum dots. © 2008 Optical Society of America.