Immediately after the attacks, the Spanish government accused the Basque separatist movement Euskadi Ta Askatasuna (Basque Fatherland and Liberty --the ETA) of responsibility for the attacks.  In the immediate aftermath, Prime Minister José María Aznar and Interior Minister Ángel Acebes, announced that the ETA was responsible and contacted media outlets to assure them of the allegations.  However, many people, both throughout Spain and around the world, believed otherwise. 

With a national election only three days away, and Spanish troops fighting in an unpopular war in Iraq, critics charged that the government accusation against the ETA was intended to deflect attention away from the link between the terrorist attacks on Spanish civilians and the fighting in Iraq.  The country had recently sent 1,300 troops to join the U.S.-led coalition in Iraq and there was widespread opposition in Spain to the war (a 2003 poll had shown that 92% of Spaniards opposed the war). 

A spokesperson for Batasuna, the political arm of the ETA, denied responsibility.  In addition, the large-scale impact, coordination, and simultaneous nature of the attacks were not characteristic of the ETA.

On March 13, 2004, an audiotape was found in a van near a Madrid mosque.  The tape claimed responsibility for the attacks by the Groupe Islamique Combattan Morrocain (Moroccan Islamic Combatant Group-GICM), believed to be inspired by Al-Qaeda’s vision of global holy war (jihad).  A mobile phone was also found in one of the bags of explosives that did not detonate, and five men, including Jamal Zougam, who was alleged to have links with the suspected leader of an Al-Qaeda cell in Spain, were arrested.

As evidence pointing to Islamic terrorists rather than the ETA emerged, anger rose against the Spanish government.  On March 13, the eve of the election, hundreds of Spaniards protested, accusing the government of manipulation and demanding transparency.  This distrust was revealed during the next day’s election, as Spain voted in the Socialist Prime Minister José Luis Rodriguez Zapatero, who withdrew all 1,300 Spanish troops from Iraq within five weeks of his inauguration.

That same day, a video was uncovered claiming responsibility for the attacks from a supposed Al-Qaeda military spokesman in Europe.  The spokesman claimed that the attacks were avenging Spain’s collaboration with the United States and its allies.

On April 3, 2004, Spanish police raided the group's holdout in Leganés, a suburb of Madrid, where seven suspected ringleaders of the attacks blew themselves up as the police closed in, killing one Spanish policeman.  By April 2005, twenty-four suspects were in jail and another sixty-five suspects had been charged with lesser crimes in connection with the bombings.  In October 2007, after a five-month long trial, a Spanish court delivered a one-hour long verdict, convicting 21 of 28 defendants.  The key perpetrators are believed to be linked to the CIGM, and although the investigation found no evidence of a direct operational link to Al-Qaeda, the CIGM was later declared a derivative structure of Al-Qaeda.