I've yet to run a patch-checking program on a computer that was fully patched. I frequently go to companies and hear all about their wonderful, automated, timely patch management systems. Then, when I audit the first computer, it's missing patches. Usually they've patched Windows and its applications, but not all the browser plug-ins. Java and Adobe Acrobat Reader are notorious for falling behind, but it isn't just them. On servers, I frequently find outdated server management software, known-to-be-vulnerable versions of backup services, and myriad unnecessary programs (if you don't need it, get rid of it).
To put it bluntly, patching sucks in so many shops. I'm not talking just being a little tardy with patching, but being years out of date. In fact, the majority of exploited, unpatched software has had vendor updates freely available for one or two years.
How to fix it? Start by finding out if your patch management system even checks for all the patches. Most don't. You can prove it by going to any workstation or server and listing every program installed on it, then checking a CVE database to see what versions are vulnerable. You'll need to do this manually, because even my absolute favorite patch-checking program, Secunia CSI, doesn't list everything despite covering more than 10,000 programs.
The first few computers you check will require a few hours of homework. But pretty soon, you'll build a quick cheat sheet of the most common applications and their appropriate versions. Or start easy and make sure every computer in your environment running Java or Adobe Acrobat Reader has the latest version and enable auto-updates, if appropriate. At least get those patched (or removed altogether if not needed). Then you can move on to less popular programs.
It's also very rare that any organization has deployed comprehensive event monitoring. Or it's enabled only on servers or domain controllers. Now remember, I just said that most attacks happen on the end-user desktop. So, uh, shouldn't those computers be among the most heavily monitored?
Event log management is horrible in most environments. The biggest threat is socially engineered Trojans, but most event log management programs are implemented so generally that there's hardly any value. They focus on dozens, if not hundreds, of other events that don't address the No. 1 problem.
Start by asking what needs to be monitored to detect malicious attacks. In many cases, that would be unexpected program execution, such as a Trojan horse program or a worm. For this sort of monitoring, I prefer to use whitelisting or application control programs. You can run most of them on one or more reference computers, and the software will usually do the software inventory and make the rules. Thereafter, the idea is to block unknown software, although that may be impractical in this day and age. Instead, you can use your whitelisting program to alert users to all the unrecognized executables.
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