Shortly after the September 11 attacks, Rodriguez was appointed Chief Operating Officer of the Counterterrorism Center. In May 2002, Rodriguez was promoted to the post of Director of the Counterterrorism Center. The Counterterrorism Center brings together case officers, operators, analysts, and technologists to work on preventing terrorism. In this capacity, Rodriguez was responsible for driving the CIA operations and the targeting analysis necessary to uncover terrorists in the Al Qaeda network. In the time period that Rodriguez was there, the Counterterrorism Center grew sharply. The number of analysts quadrupled, and the number of operations officers doubled. In 2004 Rodriguez advised the organizers of the 2004 Summer Olympics in Athens, including the chief organizer, Gianna Angelopoulos-Daskalaki, on security matters and counterterrorism.