Allgeier joined the U.S. Trade Representative in June 1980, as an international economist dealing with Asia, serving in 1981 as Director for Japanese Affairs. Between 1981 and 1985 he was Deputy Assistant Trade Representative for Asia and the Pacific. In 1985 he became Assistant Trade Representative for Asia and the Pacific. In 1989 he became Assistant Trade Representative for Europe and the Mediterranean. In 1995 he was appointed Associate U.S Trade Representative for the Western Hemisphere by USTR Mickey Kantor. As a U.S Trade Representative, Allgeier was accused of intimidating other countries to back down from tobacco control measures, including making efforts to get Korea and Taiwan to back down on marketing restrictions to children.