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Periodate oxidation reaction occurring directly on chitin has been neglected in polysaccharide chemistry so far. Herein, we present the first direct alkaline periodate oxidation of chitin, which demonstrates at the same time a novel approach for the preparation of chitin nanocrystals (ChNCs). This oxidation is based on an unprecedented selective reaction of non-ordered domains of chitin by the dimeric orthoperiodate ions (H₂I₂O₁₀⁴⁻) as the major species in alkaline surroundings. Nearly 50 wt% of non-ordered regions are dissolved after sequential accelerated partial deacetylation, periodate oxidation and β-alkoxy fragmentation, which allows the isolation of up to 50 wt% of uniform anisotropic zwitterionic ChNCs.