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A two-dimensional photonic crystal defect waveguide sensor based on CMOS-compatible silicon-on-insulator technology was designed for operation in aqueous solutions at a wavelength of 1.34 µm, by the use of the 3D Plane Wave Expansion and the Finite Difference Time Domain simulation method. An operation under water in this wavelength regime allows for a significantly smaller propagation loss in contrast to the state-of-the-art operation wavelength of photonic crystals at 1.55 µm. The sensor working principle is label-free and based on evanescent wave sensing exploiting the local refractive index change induced by the specific binding of target molecules to a capture molecules immobilized on the surface of the phontonic crystal structure. We experimentally proved the theoretical predications of our simulations and demonstrated the sensing functionality of the photonic crystal defect waveguide using the biotin-straptavidin binding system.