Palacio headed the Partido Popular's list in the June 1999 European elections, and was duly elected to the European Parliament. She also joined the European Commission on 13 September 1999, as commissioner for energy and transport, in the Prodi Commission. She also served as vice-president (jointly with Neil Kinnock), and took charge of relations with the European Parliament. She pushed forward the Galileo positioning system, and new maritime safety regulations following the "Prestige" oil spill off the coast of Galicia in November 2002.