Novel optical waveguides and methods for their fabrication are provided. The waveguides are made from polydiacetylene materials. The waveguides are made by a bilayer process wherein a film made from a soluble polydiacetylene material is applied to a substrate and a silicon-containing imaging layer is applied atop the polyacetylene layer. Thereafter a pattern is produced in the imaging layer, for example, by photolithographic methods, and the pattern is transferred to the underlying polydiacetylene layer by exposure to an oxygen plasma. Polydiacetylene waveguides greater than 0.4 microns thickness are thereby produced.