Methods, systems, and apparatuses, including computer programs encoded on computer-readable media, for secure document management including receiving, at a kernel level of an operating system, a document access instruction for a document from a user level application. A document identifier associated with the document is retrieved. Document access permissions associated with the document identifier are determined. Whether the document access instruction for the document is allowable is determined based on the document access permissions. The document access instruction is allowed to proceed if the document access instruction is allowable. The document access instruction is denied if the document access instruction is not allowable.