The Gambian winger was stretchered off at Bournemouth and Boro boss Aitor Karanka has confirmed that they fear it is a cruciate injury.
Boro are now waiting for more tests, but admit initial indications are not good.
"The doctor told me that he thought it was his cruciate, but I don't know whether it was the anterior or the posterior," said Karanka.
"So I prefer to wait for the tests and hope that he will be out for as short a time as possible.
"It is a problem with his knee, so we will just have to see what happens.
"We are hoping it is not too serious, but at this stage we do not really know. He will have the scans as soon as possible, and then we will know."
Carayol has just been recalled to the Boro side after a row with Karanka and the Spaniard had been singing his praises following some stand-out displays.
"It is a real shame because he was playing very well in the last three games," said Karanka.
"When he is like that, he is very important for the team."