In 1997, Scilingo voluntarily travelled to Spain in order to give testimony concerning these events. Nevertheless, the examining magistrate, judge Garzon afterwards had him put under arrest. An arrest warrant was also issued against 97 other Argentinean citizens.
Since then, Scilingo has gone back on his previous statements.
Scilingo was accused of attempted genocide, since the aim of the military regime at the time was to eliminate, systematically, a whole category of people, namely the opponents of the regime. Furthermore, Scilingo was also accused of terrorism and torture.
His trial was opened up on 14 January 2005 in Madrid.
Dozens of witnesses were heard, most of them survivors of the "Dirty War". On 7th of March 2005, the Prosecutor requested a sentence of 9138 years imprisonment for Scilingo.
Scilingo's defence lawyer pleaded that the Court should acquit his client for lack of evidence.
On April 19, 2005, Scilingo was sentenced to 640 years of prison.
An appeal was lodged against this decision.
On 4 July 2007 the Spanish Supreme Court increased the prison sentence to 1084 years. The increase in his sentence corresponded to the addition of offences which had not been taken into account at the time of the judgment handed down by the first trial instance, but which constituted “crimes against humanity according to international law” according to the Supreme Court. This court found Scilingo guilty of 30 murders, of one crime of illegal detention and of complicity in 255 others.
On the other hand, he was acquitted on the counts of torture for which he had also been found guilty by the first instance court.
Scilingo has been imprisoned in Spain since 2001. According to Spanish criminal code, the effective penalty he will be subject to is limited to 25 years maximum. .