Patent lawsuits are nothing new, but this one comes with a troublesome wrinkle.

Apple Inc. (NASDAQ: AAPL) is the target of another patent-related lawsuit, this time from the Wisconsin Alumni Research Foundation, or WARF. The lawsuit alleges that Apple’s A7 processor chip directly infringes a patent held by the University of Wisconsin – Madison, U.S. Patent No. 5,781,752.

Both the Apple patent and the Wisconsin patent deal with branch prediction, a technique for predicting the flow of chip instructions to make execution more efficient.

The question of infringement is one issue, but another, more important issue is the possibility that the litigation may target Apple trade secrets.

Regardless of whether or not WARF wins its lawsuit against Apple Inc. the legal action may have profound ramifications for the Cupertino-based technology firm. In the process of defending itself, Apple will likely be forced to reveal proprietary details about its A7 chip, which until now has been a closely guarded company secret. Indeed, there is already speculation in some quarters that the main purpose of the litigation is to force Apple Inc. to reveal some or all of the A7′s engineering.

As I understand it, a company can declare trade secrets to get a protective order that keeps such secrets under wraps. Don’t know how effective this is in practice.