The suit does not yet specify alleged damages.
Allen, who has a net worth estimated at $31.5 billion, was among the 38 billionaires who this month pledged to give away the majority of their wealth to philanthropy after their deaths. Last year he was diagnosed with non-Hodgkin's lymphoma, but has since completed a course of treatment.
It is the latest in a number of high-profile patent lawsuits. Oracle this month sued Google, claiming infringement of Java patents.
Apple, Nokia and HTC have also been busy and countersuing each other, and both Nokia and HTC have also been targets of recent patent suits from South Korea's Electronics and Telecommunications Research Institute (ETRI).