Marquardt began his professional mixed martial arts career in 1999, and amassing victories in various promotions before entering the "Bas Rutten Invitational 4" tournament, which was organized in such a manner that the tournament winner was to be offered a contract with the Ultimate Fighting Championship. Despite winning the tournament, Marquardt was offered no such contract. Instead, he signed with Japan's Pancrase organization, which had fostered such fighters as Ken Shamrock and Bas Rutten. In his first Pancrase fight, Marquardt lost via submission to Genki Sudo.