Methods and systems for tracking a physical object to identify or authenticate it utilizing digital fingerprints which are based on natural features extracted from a digital image of the object. Digital fingerprints do not require or rely on any labels, tags, integrated materials, unique identification characters, codes or other items that may be added to the object specifically for the purpose of identification. Consequently, the disclosed digital fingerprint techniques help to detect or prevent unauthorized alterations of documents, apparel, drugs and pharmaceuticals, etc. Further digital fingerprints can be used to better track and trace a wide variety of objects throughout the distribution chain to demonstrate their provenance and to detect counterfeit objects.