A Sanctuary is a room attached to some Institutes that is built on unhallowed ground.
The Sanctuary serves as a meeting place for Shadowhunters and Downworlders. Unlike the Institute itself, it is not built on consecrated grounds and are reverse-warded like Portals, making it possible for vampires and demons to step foot in the room. It can also be used to shelter Downworlders who need temporary protection, or to hold Downworlders or demons for interrogation.
For the Downworlders who can enter hallowed grounds, the Sanctuary was typically their entrance instead of the Institute's main doors, though this is not always the case.
The Sanctuaries doors are well-protected and warded; they can only be opened either with a key, kept only by entrusted people of the Clave, by an opening rune with a stele, or—especially for a Sanctuary's inner doors leading to the Institute—by the touch of a Shadowhunter.
Sanctuaries can be found with most Institutes built before the 1960s. When Projection magic was developed in 1958, the need for Sanctuaries diminished—at least for simple meetings, and the Sanctuary is still used for its other purposes. The established Sanctuaries were maintained even long after it fell out of fashion.
The London Institute has a Sanctuary Room.
When Axel Mortmain infiltrated the Institute, Tessa Gray, Jessamine Lovelace, and Sophie Collins—who knew where the Institute head kept the key—hid in the Sanctuary for some time before Sophie and Jessamine were forced out by Mortmain and his automatons. Alone with Tessa, Mortmain confronted her and tried to abduct her before she Changed to fake her death.
The Sanctuary is linked to the Institute through a dark corridor that slopes downward. In the 1870s, its high iron doors had a knocker and the old symbol of the Clave carved into them. The key to the doors was a slender iron key with a head in the shape an angel with outspread wings; the wings gleamed when used on the doors.
The room itself is window-less, lit by either candles in candelabras or witchlight in sconces, and has only two doors—one entrance from the Institute and another from the outer foyer. There are enormous stone pillars around the room, all carved with runes that form intricate patterns around them. The walls are also decorated with huge tapestries, each with the design of a rune. At the center of the room is a huge stone fountain of an angel with folded wings, the water pouring out of its eyes and into the circular base. It also has a great gilt-framed mirror that seems to double the size of the room in terms of appearance. Next to the fountain is a group of upholstered chairs flanked by two massive pillars.
New York Institute
The New York Institute has a Sanctuary.
In 2007, Camille Belcourt was brought to the New York Institute's Sanctuary as a captive, held there for interrogation by the Conclave. Before then, no one had ever been able to escape the Sanctuary. However, Lilith's mundane followers were able to break her out of the Sanctuary, as the room is not warded against them.
This Sanctuary is a massive, pillared stone room connected to the Institute through a narrow passageway and wide double doors. There were no windows, to keep it safe for vampires, and the whole room is lit by witchlight torches.
There were huge gouges in the stone floor from where creatures had been caged over the years. 
Los Angeles Institute
The Los Angeles Institute has a Sanctuary.
In 2012, a faerie convoy came to the Institute's Sanctuary and were met by Arthur and Julian Blackthorn, Emma Carstairs, and Diana Wrayburn. During this meeting, which the Nephilim were unprepared for despite the faeries' notice, the fey returned Mark to them in exchange for their help investigating the deaths of their people. Because they needed to communicate in secret because of the Cold Peace, the faeries—Iarlath and Kieran—suggested that they transact through the Sanctuary: the fey would go to the Sanctuary if they needed to speak to them, and if the Shadowhunters needed to contact them, they should leave messages there.
Later, when Diego Rosales went to the Institute to consult the local Conclave for his mission, he found the head, Arthur, in the Sanctuary, before he was sent away.
The Sanctuary is a massive stone-bound room in the shape of a crescent moon. The Sanctuary faces the mountains, which blocks the sun, keeping it safe for vampires. Nonetheless, the room is brightly lit by a pendant chandelier. The wooden floor is in a checkerboard style, with the squares alternating between dark and light that form the Angelic Power rune. Also in the room is a massive stone chair for the Institute's head.
The Sanctuary has two sets of doors: the one that leads outside and is the entrance for Downworlders, and the other leads into the Institute itself.
The second set of doors, like the Institute's front entrance, yields only to those with Shadowhunter blood. The doors—made of copper metal but has since become green with verdigris—has runes of protection and welcome around its framework. From inside the Institute, these inner doors can be found at the end of a corridor that led off the main entryway. This Sanctuary's protected space extends very slightly past the threshold of these doors.