The McCanns were initially placed under investigation by Portuguese police.
The parents of Madeleine McCann have lost the latest stage of a legal battle over how judges handled claims made by a Portuguese police detective.
Kate and Gerry McCann appealed to the European Court of Human Rights over the way Portugal handled their libel challenge over Goncalo Amaral’s claims.
He alleged in a book that they were involved in their daughter’s disappearance and now the couple has three months to appeal against the decision.
Mr Amaral was originally the lead detective on the case, but he was removed after criticising British police.
Madeleine disappeared from a holiday apartment in the Portuguese holiday resort of Praia da Luz in May 2007 when she was just three.
Her parents were initially placed under investigation by Portuguese police, but were removed as suspects in the case in July 2008.
The couple sued Mr Amaral for libel and were awarded £358,000 in damages by a Portuguese court, but an appeal against the decision was later upheld by the country’s Supreme Court.
In their case at the European Court, the couple said the Portuguese courts had failed to uphold their right to a private life and their presumption of innocence.
On Tuesday, however, the court said that the couple were already public figures before Mr Amaral’s book was published and that any damage to their reputation had been caused by the fact they had been declared suspects by authorities, and not by Mr Amaral’s claims.
The judgement also said that, in its ruling, Portugal’s Supreme Court had not “made comments implying any guilt… or even suggesting suspicions against” the McCanns, and so their complaint concerning their right to be presumed innocent was “manifestly ill-founded”.
A German man, Christian Brueckner, has previously been declared an official suspect in the case.
He is serving a prison sentence in Germany for separate offences and had denied involvement in Madeleine’s disappearance.
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