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Chelsea's hopes of qualifying automatically for the Champions League knockouts were dealt a blow as Atalanta came from behind to win in Bergamo.
Both sides went into this game with identical records in the league phase of this year's tournament, having won three, drawn one and lost one to sit on 10 points.
For large parts, there was little to separate them in this game, too, although Chelsea got their noses in front in the first half when Joao Pedro turned in Reece James' cross.
But Atalanta always looked like a threat going forward, with former Charlton and Everton attacker Ademola Lookman causing problems.
James shot wide in the second half, but Atalanta upped the pressure and deservedly levelled when ex-West Ham striker Gianluca Scamacca headed in a cross.
Alejandro Garnacho drove a strong effort straight at the goalkeeper, but Atalanta got the winner late on when the Blues' defence backed off Charles de Ketelaere, who took full advantage with a driven strike.
Chelsea tried to rescue a point late on, but a superb save by Marco Carnesecchi denied Pedro.
The result means Chelsea drop out of the top eight - the places that qualify automatically for the knockouts - to 11th with two league phase games remaining.
Atalanta, meanwhile, leap up to third, three points ahead of the Blues.
Chelsea analysis - concerning run continues
This was a hugely disappointing result for Chelsea as even a draw was keeping them well placed to secure the top-eight finish they need to avoid the lottery of the play-offs.
But they let their concentration slip in defence with seven minutes remaining and Atalanta took full advantage.
The Italians are in good form at the moment so this was always going to be a difficult test for the Blues, but they will be frustrated to be leaving with nothing after taking the lead.
But the bigger picture is that this continues Chelsea's concerning run of form in all competitions.
Since beating Barcelona 3-0 at the end of November they are now without a win in their last four games.
Too many changes proving costly?
Chelsea boss Enzo Maresca made five changes for this game as he continued his run of moving players in and out of the starting 11.
The changes here came after he made the same number for the loss to Leeds and six for the draw with Bournemouth prior to the trip to Atalanta.
Maresca will see rotation as necessary as he tries to manage players' workloads and compete both at home and abroad, but he insisted the core group of players remains the same for key games.
"I think tonight [in] the first XI we had eight or nine players who played against Tottenham, Barcelona and Arsenal," he said.
"If you see the five changes that we did compared to Bournemouth, it is different, but it is the eight or nine players playing Barcelona.
"The ones who played tonight are the ones playing almost all the games."
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