In 2002, Paizo Publishing acquired publishing rights and merged the Polyhedron magazine with the sister publication Dungeon to form a single magazine (issue 90 of Dungeon and issue 149 of Polyhedron were one and the same magazine, and this dual numbering continued throughout this period). This ended the association of Polyhedron with the RPGA. It also marked a major change in the magazine's focus, from a primarily Dungeons & Dragons-oriented magazine similar to Dragon to a general d20 system magazine that often featured entirely new, simple role-playing games based on this system, along with support for non-D&D d20 games such as d20 Modern. Eventually another formerly separate magazine, the Living Greyhawk Journal, briefly became a section in Polyhedron as well.
Though this version of Polyhedron had many vocal supporters, sales were poor, a situation many blamed on putting two magazines with distinct target audiences together in one somewhat higher-priced package. The Polyhedron section was removed from Dungeon as part of a major revamp of the latter magazine in 2004 and Polyhedron is no longer published in any form.
For a short time in 2006 and 2007, Wizards of the Coast used the name "Polyhedron" for a Dungeons & Dragons email newsletter. As far as can be determined at this time, the newsletter consisted of advertisements for the company's Web site and does not seem to have been particularly popular.