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Independent citing officer Ken Pattinson reported him for illegally making contact with the eye or eye area of Wasps and England forward James Haskell with his hand in last Saturday's clash at Franklin's Gardens.
Haskell is currently banned after receiving a one-week suspension for striking an opponent with his head during Wasps' home defeat by Worcester six days earlier.
The England star, though, could still have missed Wasps' trip to Leicester tomorrow night due to the eye injury sustained against Northampton.
Best, 29, joined Saints from Ulster earlier this summer.
He has been charged "with an act contrary to good sportsmanship under law 10.4k".
He must now appear before a three-man Rugby Football Union disciplinary panel chaired by Judge Jeff Blackett, assisted by Peter Budge and Jeff Probyn, in London next Tuesday afternoon.
The range of punishments for Best's alleged offence vary from a six-week ban to a maximum of two years.
Best's Northampton team-mate, hooker Dylan Hartley, received a six-month suspension last year after being found guilty on two counts of eye-gouging.
The incidents also happened against Wasps, and also involved Haskell, together with Wasps flanker Johnny O'Connor.
Hartley's suspension meant he was ruled out of contention for a place in England's 2007 World Cup squad.
Blackett chaired Hartley's hearing, and afterwards he said: "Contact with an opponent's eyes is a serious offence because of the vulnerability of the area and the risk of permanent injury.
"It is often the result of an insidious act, one which is abhorred by players.
"Such offences carry a substantial punishment to protect players, deter others and remove culprits from the game to ensure that they learn the appropriate lesson."
Northampton have so far not reacted to news of Best's citing.
He has started all three of Saints' Premiership games so far this season, and would be expected to keep his place for Saturday's Vicarage Road appointment with Saracens.
Best has won 18 caps for Ireland. He made his debut against New Zealand in 2005, and featured as a substitute during the 2007 World Cup against Georgia, France and Argentina.