A digital signature service generates digital signatures for documents independent of the program used to transmit the documents. The digital signature service may operate as a Web server application, or as a client application on a user's computer. The digital signature service imports a certificate specific to a user. To digitally sign a document, the user identifies a document, and the digital signature service generates a single signature file that includes the user's certificate, the document, and the digital signature. With the signature file, the user may now store and/or transmit the file using any program while maintaining the integrity and authenticity capabilities associated with digital signatures. The digital signature service also permits multiple digital signatories to a single document. A secure document repository, implemented on a Web Site, is also disclosed.