The incident, which occurred in the 65th minute of Munster's 26-17 victory at Murrayfield on Sunday, was missed by match officials, but has now been picked up by the citing commissioner, Italy's Alberto Recaldini.
O'Gara appeared to kick out at Cox from behind, sparking a scuffle between numerous players from both sides.
If found guilty, 35-year-old O'Gara could find himself banned for Sunday's crucial Heineken Cup Pool 1 decider against Racing Metro and some or all of Ireland's RBS 6 Nations campaign, which begins away to Wales on February 13.
The citing, under law 10.4(c), carries a low end entry point of a four-week ban, with a top-end sanction of anywhere between 12 weeks and a year should he be found guilty.
Estebanez also in hot water
Racing Metro centre Fabrice Estebanez has also been cited for allegedly striking Saracens and England wing David Strettle with his arm during his side's 37-28 defeat on Saturday.
His charge under law 10.4(a) - striking an opponent with the fist, arm... head or knee - carries a low-end entry point of a two-week ban with a top-end entry point of at least eight weeks.
Stade Francais lock Juan Cruz Guillemain faces a more serious charge under the same law after allegedly striking Grenoble's Fabien Alexandre with his head. The top-end entry point for Guillemain's citing is from 16 weeks to two years.
All three cases will be heard in Dublin on Thursday, with His Honour Judge Jeff Blackett passing judgement on O'Gara while Ireland's independent Judicial Officer Pat Barriscale will rule on both Estebanez and Guillemain.
Source : http://www1.skysports.com/rugby-union/news/15185/8397230/Munster-s-Ronan-O-Gara-has-been-cited-for-allegedly-kicking-Edinburgh-s-Sean-Cox