Microsoft filed a lawsuit in federal court today alleging that has violated several of its software patents.

The lawsuit, which I have embedded at the end of this post, says that the sales application company has violated nine of Microsoft’s patents, including a “method and system for mapping between logical data and physical data”, a “system and method for providing and displaying a web page having an embedded menu,” and “automated web site creation using template driven generation of active server page applications.”

Microsoft and Salesforce don’t compete directly on operating systems or office software, which are Microsoft’s biggest sources of revenue. But Microsoft does offer sales software, and both companies have platforms for web-based applications. Salesforce chief executive Marc Benioff (pictured above) is also a frequent (and entertaining) critic of Microsoft as a dinosaur that doesn’t understand the importance of cloud computing — for example, when comparing their cloud platforms, he said of Microsoft, “They hate everybody and we love everybody.

Microsoft emailed VentureBeat the following statement from Horacio Gutierrez, the company’s corporate vice president and deputy general counsel of Intellectual Property and Licensing:

Microsoft has been a leader and innovator in the software industry for decades and continues to invest billions of dollars each year in bringing great software products and services to market. We have a responsibility to our customers, partners, and shareholders to safeguard that investment, and therefore cannot stand idly by when others infringe our IP rights.

A Salesforce spokeswoman declined to comment, but Cnet’s Ina Fried points out that Salesforce was probably talking about Microsoft in a regulatory filing from January:

During fiscal 2009, we received a communication from a large technology company alleging that we were infringing upon some of their patents. We continue to analyze the potential merits of their claims, the potential defenses to such claims and potential counter claims, and the possibility of a license agreement as an alternative to litigation. We are currently in discussions with this company and no litigation has been filed to date. However, there can be no assurance that this claim will not lead to litigation in the future. The resolution of this claim is not expected to have a material adverse effect on our financial condition, but it could be material to the net income or cash flows of a particular quarter.

MSFT vs Sales Force Complaint

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