Proton beam writing is a direct write lithographic technique that can be used to fabricate optical waveguides in a range of materials including polymer and glass. In this paper we demonstrate the proton beam writing method for fabricating waveguides in PMMA, and in Foturan photosensitive glass using a single step process of end of range refractive index modification. Both these materials are of considerable importance for bio and chemical sensing applications since they can both be directly micromachined either optically using photolithography or by using proton beam writing. The waveguides fabricated in these materials have been characterized optically to determine the propagation loss and the refractive index. (c) 2005 Elsevier B.V. All rights reserved.