Came across this little piece of trivia on IMDB:

At the film's conclusion, after the credits, we see Kate and Sean standing in their garden waving good-bye. Maureen O'Hara turns to John Wayne and whispers something in his ear, evoking a priceless reaction from Wayne. What was said was known only to O'Hara, Wayne and director John Ford. In exchange for saying this unscripted bit of text, O'Hara insisted that the exact line never be disclosed by any involved parties. In her memoirs she says that she refused to say the line at first as she "couldn't possibly say that to Duke", but Ford insisted, claiming he needed a genuine shock reaction from Wayne. The line remains a mystery to this day.