The Richard Desmond-owned stable agreed to pay undisclosed substantial damages to Gerry and Kate McCann, which will be put towards the , after accepting that there is no truth behind a number of articles it published.
The papers printed hundreds of articles in the last 11 months about the disappearance of Madeleine McCann, including stories linking Madeleine's parents to being involved with or causing the death of their daughter.
Express Newspapers faced a highly expensive, but until now, unpublicised, court case brought about by the couple's legal representatives, Carter-Ruck, for defamation.
, said the newspaper group's coverage of the couple including "wildly and grossly defamatory articles".
The McCanns identified more than 100 articles that they deemed to be defamatory in the last year, of which 42 were published in the .
The printed apologies, which are expected to be repeated in The Star Sunday and Sunday Express this weekend, will be read out in the High Court today.
The newspapers involved have agreed to remove from its websites all articles about the disappearance of Madeleine McCann, who is believed to have been abducted from a holiday complex in Praia da Luz, Portugal on May 4 last year.
An extract from one of the front page apologies reads: "[The Daily Express] accepts a number of articles in the newspaper have suggested that the couple caused the death of their missing daughter Madeleine and then covered it up.
"We acknowledge that there is no evidence whatsoever to support this theory and that Kate and Gerry are completely innocent of any involvement in their daughter's disappearance...we are truly sorry to have to have added to [Kate and Gerry's] distress."
Roy Greenslade, former editor of the Daily Mirror and media commentator at The Guardian, described the as "an amazing-stand down", and that Express Newspaper's coverage of the McCann case could remove reader's sense of trust.
He said: "I think when people realise that more than 100 stories have been complained about as being grossly defamatory, it will annihilate the Express readers' sense of trust and credibility in their newspaper."
In a further attack on Express Newspaper's coverage, Greenslade added: "This was no journalistic accident, but a sustained campaign of vitriol against a grief-stricken family.
"The stories were not merely speculative, but laced with innuendo, which continually made accusations against the McCanns on the basis of anonymous sources and without hard evidence."
The apology was welcomed , which was the first organisation to hold a public debate on the media treatment of the McCann family.
Charlie Beckett, Polis director, said the apology possibly marked the moment when the tide turns against certain media excesses that have been growing in recent years, which have commodified tragic events.
He said: "Most of the media had gone a bit mad over this story while a minority had lost all their editorial senses.
"A combination of the McCann's public relations campaign, the internet, the Portuguese press and a loss of UK media inhibition had combined to 'commodify' a tragic human story.
"Vast amounts of innuendo and tenuous rumour were printed (and broadcast) without fact-checking or proper contextualisation.
"The fact that the Express will pay the price should act as a warning to others who have strayed in similar ways.
"I hope that other media outlets who have dabbled in mindless and cruel speculation will not simply be grateful that the struggling Express group has taken the hit on their behalf."
The apology is first major one by a newspaper since the Daily Mirror said sorry to the Queen's Lancashire Regiment after it accused it of torture after publishing fake pictures of UK troops abusing Iraqi prisoners. The paper's editor Piers Morgan resigned over story and the paper ran the full front page headline "Sorry.. we were hoaxed".
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