The New York Institute refers to the Shadowhunter Institute in New York, currently co-headed by Clary Fairchild and Jace Herondale. It is where the New York Conclave meet, provide protection to Shadowhunters, and, in some cases, mundanes and Downworlders in need of their help.
The Institute is said to look like an old gothic cathedral. As it is covered by a glamour, mundanes see the church abandoned and almost in ruins because of it. The Institute also has a glamoured brass plate next to the entrance—a set of double doors—with the Institute's name etched into it.
The interior of the Institute is enormous, with several corridors and hallways adorned with arches. The nave of the Institute, still with its pews, is also well kept, with witchlight and tapers in candelabras as its main source of light.
The library in the Institute is filled with hundreds of books. They surround the circular room and the shelves go up two floors. There is a desk in the center which Hodge often sat in when he lived there. There are multiple chairs throughout the room to sit and read in. It is circular because it is built into a tower of the Institute. The second floor gallery held things of importance, with some on display: there were books related to dangerous demon magics, necromancy, demon pox, and various other subjects. In between each bookshelf was a glass case, each holding beautiful treasures in them: the faerie rings, a crystal bird, a large crown, and the clockwork angel.
The training room is located in the attic of the Institute. There are beams located twenty feet in the air that are used to teach Shadowhunters balance and flexibility. A small changing room is located just off the training room.
The greenhouse is at the top of the Institute, with a spiral staircase leading up to it. It is filled with dozens of plants that are used for medicinal purposes, some that only grew in Idris. There is no particular pattern to the layout of the greenhouse. Green hedges with blue violet blossoms, vines with buds like jewels, moonflowers, angel's trumpets, four o' clocks, wolfsbane, midnight flowers, and several other types of flowers filled the space, giving it a scent of springtime though Shadowhunters note that it smelt like Idris. The dome's ceiling looked like an "inverted lake." There is a stone bench in the center, next to a "stone-bound rock pool" with trees surrounding it.
The Institute has an infirmary—a huge room with an arched wooden ceiling with murals. It also has an elevator which resembled a gilded birdcage, its gate and walls made of black metal decorated with bits of gilt; one of the walls is also mirrored. Additionally, it has several rooms in its residential wing that can hold at least two hundred guests, mostly Shadowhunters who request lodging.
Since it was built in the early days of the Nephilim, it still has a Sanctuary, a section of the Institute that is outside the protection of hallowed ground, used to allow Shadowhunters and the Downworlders who cannot enter hallowed ground to hold meetings within the Institute. Upon the creation of Projecting, Sanctuaries have become less used, and some newer Institutes no longer even have them.
- Beatriz Mendoza (tutor)
- Hodge Starkweather † (former tutor)
- The appearance of the Institute is based on St. Patrick's Cathedral.
- Hodge Starkweather was exiled here because of his allegiance to the Circle during the Uprising.
- Sometime after she and Jace took control, Clary had a computer—forbidden under Nephilim tradition—installed in the strategy room of the Institute.
- Vampires are the only beings who are completely incapable of stepping into the Institute because of the hallowed ground it is built upon; thus, they usually converse with its residents from the Sanctuary or through Projection. However, some time after 2007, Magnus Bane wove special spells to allow vampires to enter and walk through certain parts of the Institute, particularly for Lily Chen.
- According to an answer from Cassandra Clare released by a reader, Isabelle and Simon ran the Institute while Jace and Clary were on a mission in Faerieland in Lord of Shadows.