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Unlike other crystals, the counter intuitive response of bismuth germanate crystals (Bi4Ge3O12, BGO) to form localized high refractive index contrast waveguides upon ultrafast laser irradiation is explained for the first time. While the waveguide formation is a result of a stoichiometric reorganization of germanium and oxygen, the origin of positive index stems from the formation of highly polarisable non-bridging oxygen complexes. Micro-reflectivity measurements revealed a record-high positive refractive index contrast of 4.25 × 10-2. The currently accepted view that index changes > 1 × 10-2 could be brought about only by engaging heavy metal elements is strongly challenged by this report. The combination of a nearly perfect step-index profile, record-high refractive index contrast, easily tunable waveguide dimensions, and the intrinsic high optical non-linearity, electro-optic activity and optical transparency up to 5.5μm of BGO make these waveguides a highly attractive platform for compact 3D integrated optics.