The trio all returned from injuries in recent weeks and have given van Gaal options over the busy Christmas period. Smalling picked up a muscle injury against Southampton but was able to return off the bench against Tottenham on Sunday.
Luke Shaw also made a brief cameo at White Hart Lane after missing six weeks with an ankle injury whilst Rafael played 45 minutes after returning on Boxing Day against Newcastle.
With Phil Jones and Jonny Evans fit, the manager now has options but says he needs his players to get their match rhythm back over the coming weeks.
Speaking ahead of the New Year’s Day game at Stoke City, Van Gaal said: “There are players coming back, we have seen the first signs of that in the last two games with Rafael, Chris Smalling and Luke Shaw.
“They don’t have any match rhythm and that’s my problem, it’s the case with a few players. We played three or four games in the space of a week, so we need these players now more than ever. It’s now difficult for me to select the team.”