Barcelona were stunned by Roma in the Champions League on a torrid night at the Stadio Olympico in Italy.
The Serie A giants went into the match 4-1 down from the first leg but goals from Edin Dzeko, Daniele De Rossi and Kostas Manolas left them reeling.
Messi was unable to propel Barcelona through to the next round with the Argentina international a subdued figure throughout the match.
And Spanish website Don Balon say Messi now fears for the Ballon d'Or.
Messi has won the accolade five times throughout his career, the same amount as Real star Cristiano Ronaldo.
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Barcelona news: Lionel Messi fears Roma defeat will damage his Ballon d'Or chances
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However, he now faces a fight to scoop the prize - particularly with Ronaldo and Real going strong.
Though dished out to individual players, voting for the Ballon d'Or usually takes team performance into consideration.