Following the poor results obtained by IU in that elections (20 deputies in 1996, and 8 in 2000), Llamazares announced his intentions to run for the post of General Coordinator in the Coalition's sixth Federal Assembly due to be held December that year.

Llamazares was re-elected General Coordinator in the seventh Federal Assembly of IU held in December 2003, being opposed by Luis Carlos Rejon, then Deputy for Cordoba, who was backed by several regional minorities, along with the new leftist faction "Espacio Alternativo", and Juan Manuel Sanchez Gordillo Mayor of Marinaleda, Seville, who was supported by the more radical factions of IU (mainly Corriente Roja and CUT).

In the 2004 general election, Llamazares was elected Deputy for Madrid (as it is tradition for the Prime Ministerial Candidates of the national parties to be candidates for Madrid), but IU obtained its worst result ever with only 3 seats in Congress (5 in coalition with Initiative for Catalonia Greens).

[1] During the electoral campaign, Llamazares announced he will not re-run as candidate for General Coordinator of IU in the following Assembly, supposedly scheduled for autumn that year.

In July 2007, Llamazares announced he will intend to run once more as candidate for prime minister, a decision that caused several controversies inside the organization, specially amongst the Communist Party of Spain, and other sectors considered to be on the left of IU, along with that it was announced that the upcoming general assembly will be postponed to after the General Election, scheduled for March 2008.

On October, Marga Sanz, a member of the Communist Party of Spain's Standing Committee and its General Secretary in the Valencian Community, announced her intention to run against Llamazares for IU's nomination to prime ministership.

In 2009, he sought to publicly condemn Pope Benedict XVI for having argued that condoms may in fact do more harm than good in the fight against AIDS.

[2] On 15 January 2010, the Federal Bureau of Investigation published digitally-aged pictures of Osama bin Laden and Atiyah Abd Al-Rahman on its website which they claimed were produced using cutting-edge technology.