A method and system for automatically verifying the authenticity of documents is provided. The method has: scanning a document to be verified in the visible and ultraviolet light spectrum; detecting in the scanned document digital watermarks printed with visible and ultraviolet ink; decrypting the marks, thereby obtaining an ultraviolet mark identifier and a variable data mark identifier; validating the percentage of the mark by checking for the presence of the digital watermark in different areas of the scanned document; comparing the mark identifiers obtained with mark identifiers stored in a database; and determining the validity of the document on the basis of the comparison. The invention allows the validity of the data printed in the document to be checked automatically, reducing the possibility of the undetected falsification, modification or total or partial alteration of a document.