Ничего не скажу про MySQL, но, например, можно сделать так:

if ( ServletFileUpload.isMultipartContent(req) ) {

    FileItemFactory factory = new DiskFileItemFactory();
    ServletFileUpload upload = new ServletFileUpload(factory);
            
    List fileItems = upload.parseRequest(req);

    Iterator i = fileItems.iterator();

    while ( i.hasNext() ) {

        if ( !fi.isFormField() ) {
            Class.forName(dbDriverClass);
            Connection conn = DriverManager.getConnection(dbConnString, dbUserName, dbUserPassword);
            String sql = "INSERT INTO files (contenttype, file) VALUES (?, ?);";
            PreparedStatement ps = conn.prepareStatement(sql);
            ps.setString(1, fi.getContentType());
            ps.setBinaryStream(2, new ByteArrayInputStream(fi.get()), (int)fi.getSize());
            ps.executeUpdate();
            ps.close();
            conn.close();
        }

    }
}