On the back of the news that Microsoft (MSFT) is suing Motorola (MOT) for patent infringments related to Android, Steve Ballmer tells the Wall Street Journal that HTC is paying a license fee for its use of Android…and that other Android manufactures may be forced to do the same.

WSJ: Is that difficult in an environment where Android is free?

Mr. Ballmer: Android has a patent fee. It’s not like Android’s free. You do have to license patents. HTC’s signed a license with us and you’re going to see license fees clearly for Android as well as for Windows.

WSJ: It doesn’t seem like the license fee alone is a big financial opportunity for Microsoft.

Mr. Ballmer: It’s one of the opportunities. One.

Steve Ballmer alluded to this new patent fee when he spoke to us in May:

[cnnmoney-video vid=/video/technology/2010/05/21/tm_microsoft_mobile.fortune]

In a few strange twists of fate, HTC (who also make Windows 7 phones) was sued by Apple (AAPL) over mobile patents related to smartphones.   To bolster its patent portfolio in its fight against Apple, HTC went to Microsoft and bought licenses to patents that they hope will have arbitrators throwing out Apple’s disputes.  Those licenses also indemnify HTC from Microsoft’s current campaign to sue Android hardware manufacturers.

Now, every time someone buys an HTC Incredible or EVO, Microsoft makes a few bucks.  That’s got to be disappointing to the anti-Microsoft crowd.

The third biggest Android phone maker on earth, Samsung, also make Windows 7 phones.  If they do have any run-ins with Microsoft, expect another lawsuit out of Redmond to come their way.