For some time now, Google has scanned web sites for potentially malicious software that can download and install itself on a web site visitor’s computer simply by viewing a page. If Google detects a potential threat, it displays a warning message when a user clicks a result link (you can see an example of this warning message by clicking this link).
Matt Cutts says that a number of people have protested that their sites are getting improperly flagged by this malware warning. He writes:
“I’ve checked out a quite a few ‘we don’t have any malware’ reports at this point, and I’ve yet to see a false positive – the sites in question have each had some malware on them. But this change is also relatively new, and we’ll keep working on ways to help site owners diagnose if their site has been hacked and is distributing malware. Maybe we can show some of the urls that appear to have malware in our webmaster console, for example. In general, I’d check file-modification times for the pages on your site to see if someone has changed your pages recently.”
Matt then goes on to list the steps you should take if your web site is clean and Google really is incorrectly flagging your site in this blog post. This recent Search Engine Land post also has more information on how you can get Google Webmaster Central confirmation of a problem.