The much-maligned European court of human rights has this week shown itself at its very best: standing up for the rights of an individual who has been denied justice for almost nine years since he was abducted, secretly detained, and tortured under the CIA's rendition program.

Khaled El-Masri, a German national, was seized by Macedonian security officers on 31 December 2003, at a border crossing, because he had been mistaken for an al-Qaida suspect. He was held incommunicado and abused in Macedonian custody for 23 days, after which he was handcuffed, blindfolded, and driven to Skopje airport, where he was handed over to the CIA and severely beaten.

The CIA stripped, hooded, shackled, and sodomized el-Masri with a suppository – in CIA parlance, subjected him to "capture shock" – as Macedonian officials stood by. The CIA drugged him and flew him to Kabul to be locked up in a secret prison known as the "Salt Pit", where he was slammed into walls, kicked, beaten, and subjected to other forms of abuse. Held at the Salt Pit for four months, el-Masri was never charged, brought before a judge, or given access to his family or German government representatives.

The CIA ultimately realised that it had mistaken el-Masri for an al-Qaida suspect with a similar name. But it held on to him for weeks after that. It was not until 24 May 2004, that he was flown, blindfolded, earmuffed, and chained to his seat, to Albania, where he was dumped on the side of the road without explanation.

In December 2005, German Chancellor Angela Merkel told a press conference – while then Secretary of State Condoleezza Rice stood by her side – that the United States had admitted it had made a mistake. But the US government still refused to acknowledge its shameful conduct in el-Masri's case and waged a successful campaign to prevent other governments from disclosing the truth.

El-Masri's subsequent search for justice has repeatedly been thwarted. The United States succeeded in getting el-Masri's US lawsuit dismissed on "state secrets" grounds without even responding to his allegations; in 2007, the US supreme court declined to review that dismissal. The Macedonian government resorted to bald-faced lies, claiming that it played no role in his detention or abuse, despite overwhelming evidence confirming his account. The German government refused to disclose what it knew about el-Masri's case, and apparently caved to US pressure not to seek extradition of CIA officials involved in el-Masri's rendition.

Today, the European court of human rights delivered a measure of justice to el-Masri. It vindicated his account of his ill-treatment, and unanimously found that Macedonia had violated his rights under the European Convention, including by transferring him to US custody in the face of a risk of ill-treatment, and facilitating and failing to prevent his being subjected to CIA "capture shock" at Skopje airport.

This is the first court to comprehensively and specifically find that the CIA's rendition techniques amounted to torture. The decision stands in sharp contrast to the abject failure of US courts to deliver justice to victims of US torture and rendition.

Both the United States and Macedonia must now issue el-Masri a full-scale public apology and appropriate compensation. Macedonia should also commit to an internationalized investigation capable of holding its officials accountable. There are plenty of examples of such inquiries into national issues that are too politically charged to handle unaided: Northern Ireland's 1997 Independent International Commission on Decommissioning (IICD) included members from Canada, the United States, and Finland.

But Europe's work is not over yet. Macedonia was not the only European country complicit in CIA renditions. A 2006 inquiry by Swiss Senator Dick Marty implicated 14 European governments – including the United Kingdom – in the CIA's "spider's web" of rendition operations. But with the exception of Italy, whose highest court recently upheld the convictions of US and Italian officials for involvement in rendition, neither the UK nor other complicit countries – including Lithuania, Romania, and Poland, which hosted secret CIA prisons – have conducted effective investigations capable of holding officials accountable for their participation in rendition.

The human rights principles at stake extend to the use of the death penalty. European governments are prohibited from transferring criminal suspects to the United States if they risk execution; yet Abd al-Rahim al-Nashiri, a Saudi national, was secretly flown to Guantánamo Bay after being held in secret CIA prisons in Romania and Poland. He now faces a possible death sentence after a trial by military commission that does not meet international standards.

The European court's decision in the el-Masri case is a clarion call for accountability for the flagrantly illegal CIA rendition program.

The time has come for European governments to stand up to the United States and break the conspiracy of silence, regardless of the diplomatic consequences. As former Human Rights Commissioner for the Council of Europe, Thomas Hammerberg, rightly said on the occasion of the tenth anniversary of the 11 September attacks: