We report here a procedure for the functionalization of SiO 2-coated, SiONx waveguides for biological assays. Surface functionalization occurs by self-assembly of an amine-terminated silane monolayer on the waveguide, followed by partial chemical modification with functionalized polyethylene glycol (PEG) groups. Functionalized surfaces were characterized by atomic force microscopy and contact angle measurements. When combined with a BSA blocking step, these functional PEG surfaces significantly reduced non-specific binding and allowed for specific binding to occur. An antibody sandwich assay for detection of Bacillus anthracis protective antigen was used to validate these surfaces for sensing applications.