Morientes was a surprise omission at UEFA Euro 2000, but played at Euro 2004 in Portugal, where he scored one of only two goals that the side could manage, in a subsequent group stage exit. He also played for the nation during the 2006 World Cup qualifiers; however, due to his poor club form for Liverpool, he was not chosen by national team coach Luis Aragonés in the final squad for the tournament, although he was part of an initial 31-man list.