In the aftermath of last month's trial, when Terry was acquitted of racially abusing Ferdinand's brother, Anton, The United defender responded to a Tweet that characterised Chelsea defender Ashley Cole, who was a defence witness, as a "choc-ice".
The term is is commonly understood to mean "black on the outside, white on the inside", and was a reference to Cole's testimony in court, in which he said he never heard Terry make a racist remark to Ferdinand during the match in question at Loftus Road in October.
Ferdinand was charged on Monday and had until 4pm on Thursday to respond to the FA.
A statement issued on the FA's website, www.thefa.com, read: "Manchester United's Rio Ferdinand has today denied an FA charge of improper conduct in relation to comments posted on Twitter.
"The allegation is that the player acted in a way which was improper and/or brought the game into disrepute by making comments which included a reference to ethnic origin and/or colour and/or race.
"The player has requested a personal hearing."