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Gilchrist, 24, captained Scotland twice on their summer tour - against Argentina and South Africa.
The only uncapped player selected by head coach Vern Cotter is centre Mark Bennett, one of 17 Glasgow Warriors players included.
However, former captains Kelly Brown and Al Kellock are absent.
"You only have to meet him and talk to him to understand that he is a leader," said Cotter of his skipper. "People follow him.
"He likes making decisions, he likes being involved and creating outcomes. Even if he is only 24, he shows these qualities, I think he was born a leader and he gets the role."
Saracens lock Jim Hamilton, capped 56 times, is another experienced player to miss out, as does Castres wing/centre Max Evans.
Glasgow number eight Adam Ashe, 21, keeps his place after a late call for the final game of the summer tour; a 55-6 mauling by the Springboks.
Hooker Fraser Brown is another player looking to add to his solitary cap, while prop Gordon Reid, flanker Blair Cowan and fly-half Finn Russell are retained after making their debuts in June.
Matt Scott, David Denton, Ryan Grant, Ruaridh Jackson, Ross Rennie, Jon Welsh and Ryan Wilson are sidelined by injuries.
"The most important thing for us, other than showing improvements in key areas, is developing an attack that will give us opportunities to score tries or earn points through teams being forced to infringe," said Cotter.
"We want to develop, and impose, our style, will, and strategy on our opposition."
The series kicks off with Argentina visiting Murrayfield on 8 November, with New Zealand in Edinburgh a week later, while the Tonga clash is at Kilmarnock's Rugby Park on 22 November.
"Argentina will offer us a very stern test, especially at scrum time," said Cotter. "They have good variety and move the ball well from nine, through the middle of the paddock and out the back.
"The All Blacks have just won the Rugby Championship and are the best team in the world, so we'll have to be on our toes.
"Tonga will be the final big test psychologically, having come through two big games. It's essential that we show maturity, mental strength and adaptability throughout the series.
"We have a good group, but the most important thing is that we play for each other, we play for the shirt, and we enjoy what we do."
Allan Dell and Hamish Watson of Edinburgh and Glasgow's Zander Fagerson have been invited to train with the squad.
Scotland squad:
Forwards: Adam Ashe (Glasgow Warriors), Johnnie Beattie (Castres), Fraser Brown (Glasgow Warriors), Blair Cowan, Geoff Cross (both London Irish), Alasdair Dickinson, Ross Ford (both Edinburgh), Chris Fusaro (Glasgow Warriors), Grant Gilchrist (Edinburgh, capt), Robert Harley, Jonny Gray (both Glasgow Warriors), Richie Gray (Castres), Scott Lawson (Newcastle Falcons), Kieran Low (London Irish), Euan Murray, Gordon Reid (both Glasgow Warriors) Alasdair Strokosch (USA Perpignan), Tim Swinson (Glasgow Warriors).
Backs: Mark Bennett (Glasgow Warriors), Chris Cusiter (Sale Sharks), Alex Dunbar (Glasgow Warriors), Dougie Fife, Tom Heathcote (both Edinburgh), Stuart Hogg (Glasgow Warriors), Greig Laidlaw (Gloucester), Sean Lamont, Sean Maitland, Finn Russell, Henry Pyrgos, Tommy Seymour (all Glasgow Warriors), Duncan Taylor (Saracens), Tim Visser (Edinburgh), Duncan Weir (Glasgow Warriors).
Edinburgh lock Grant Gilchrist has been named captain of Scotland's 33-man squad for the autumn Tests against Argentina, New Zealand and Tonga.