From: Matthew 17:9a, 10-13
The Transfiguration (Continuation)
 And as they were coming down the mountains,  (And) the disciples asked Him (Jesus), "Then why do the scribes say that Elijah must come?"  He replied, "Elijah does come, and he is to restore all things;  but I tell you that Elijah has already come, and they did not know him, but did to him whatever they pleased. So also the Son of Man will suffer at their hands."  Then the disciples understood that He was speaking to them of John the Baptist.
10-13. Malachi 4:5 (3:23 in the Hebrew) speaks of the coming of Elijah the prophet before "the great and terrible day of the Lord", the Judgment Day. When Jesus says that Elijah has already come, He is referring to St. John the Baptist, whose mission it was to prepare the way for the First Coming of the Lord, the same as Elijah will have to do prior to His last coming. The scribes failed to grasp the meaning of the prophecy of Malachi; they thought it referred simply to the coming of the Messiah, the First Coming of Christ.
Source: "The Navarre Bible: Text and Commentaries". Biblical text taken from the Revised Standard Version and New Vulgate. Commentaries made by members of the Faculty of Theology of the University of Navarre, Spain. Published by Four Courts Press, Kill Lane, Blackrock, Co. Dublin, Ireland. Reprinted with permission from Four Courts Press and Scepter Publishers, the U.S. publisher.