Methods and systems for detecting undesirable computer files based on scanning and analysis of information contained within an associated digital certificate chain are provided. According to one embodiment, a file having associated therewith a certificate chain is received. A type and structure of the file are identified. A location of the certificate chain is determined based on the identified type and structure. A signature of the file is formed by extracting a targeted subset of information from the certificate chain. The file is evaluated by comparing the signature with a set signatures having a known desirable or undesirable status. The file is classified based on a result of the evaluating into a category of multiple categories, including one indicative of an associated file being an undesired file or a file suspected of being undesired. The file is handled in accordance with a policy associated with the category.