In the western bays the arches between the mullions of the triforium are cinquefoiled (they are trefoiled in the eastern bays), and the bases are much shorter.

All the mullions of the clerestory windows have capitals. The two central mullions, as in the nave, are thicker than the rest. They rise also to the head of the arch. The two outer lights are coupled by an arch above them. The upper lights are broken up into a number of divisions, vertical and parallel in the choir proper, slightly varied in direction in the retro-choir. The mouldings are as elaborate and as carefully subordinated as in the earlier work of the nave.

Below the transom dividing triforium from clerestory is a row of panelling divided by the mullions of the triforium, which, as in the nave, are merely a continuation of the mullions of the clerestory. The arches of the triforium are not ornamented with a gable, as in the nave, but with a moulding decorated with crockets and ending in a rich finial. The capitals of the main vaulting shafts are very curious. They consist of an ordinary row of carved foliage with three pendants ending in small carved figures with cinquefoiled arches between them. The outer mouldings of the main arches are cut short by the small outer vaulting shafts. A little way below them are small heads, as in the nave. The capitals of the main arches are like those of the nave, but their foliage is more disconnected. On the north side of the choir are figures on the capitals. Mr Browne, the enthusiastic and laborious historian of the minster, has supposed these figures to represent scenes in the rebellion in which Scrope took part. If the ordinary date given to the choir be accepted, it was built before that rebellion. But Mr Browne has endeavoured to prove that the choir was built later than is usually supposed. It is impossible in this book to do more than mention the controversy started by him, and to say that, in the opinion of Professor Willis and others, he has not made out his case. In the four eastern bays brackets and canopies for statues are attached to the vaulting shafts below the capitals of the piers. Those east of the altar were badly altered and restored after the fire of 1829. It should be mentioned two eastern bays are narrower than the rest for the better support of the eastern wall of glass, and the western bays for that of the tower. In the spandrels of the main arches are coats of arms, mainly of benefactors. The following is a list of these, taken from Murray's handbook to the minster, and beginning at the north-east end of the choir:—

1.Two keys in saltire—Chapter of York.
2.Six lions rampant—Ulphus.
3.Three lions passant guardant, a label of three points, each charged with three fleur-de-lis—Thomas, Duke of Lancaster.
4.Three lions passant guardant, a border—Edmund of Woodstock.
5.A bend between six lions rampant—Bohun.
6.Checky, a fess—Clifford.
7.A cross floré—Latimer.
8.Barry of ten, three chaplets—Greystock.
9.The instruments of the Passion.
10.Three estoiles of six points, a border—St. Wilfrid.
11.Two keys in saltire, a border engrailed—St. Peter.
12.Two swords in saltire, a border engrailed—St. Paul.
13.Seven lozenges conjoined, 3, 3, and 1—St. William. (Archbishop and Patron Saint.)
14.On a bend, a lion rampant—Musters.
15.A chief, three chevronelles interlaced in base—Fitz-Hugh.
16.On a saltire, a crescent—Neville.
17.
18.		A fess dancette—Vavasour.

Those on the south side, beginning at the west end, are as follows:—

1.A cross—St. George.
2.A cross floré between five martlets—Edward the Confessor.
3.Three crowns, 2 and 1—King Edwin.
4.Barry of six, on a chief, two pallets between as many esquires based—Mortimer.
5.Six lions rampant, 3, 2, 1, with a horn on the west side of the shield (referring to the famous gift of lands)—Ulphus.
6.A lion rampant—Percy.
7.Quarterly, 1 and 4 a lion rampant for Percy, 2 and 3 three luces hauriant for Lucy—Percy.
8.A bend, a label—Scrope of Masham.
9.Six osier wands interlaced in cross—Bishop Skirlaw.
10.A bend, a border charged with mitres; over all a label—Archbishop Scrope.
11.Three water bougets—Roos.
12.A saltire—Neville.
13.On a cross five lions passant guardant—City of York.
14.Three fusils in fess—Montague.
15.A fess between six cross crosslets—Beauchamp.
16.A lion rampant—Percy.
17.France (ancient) and England (quarterly), with a label of three points—Edward, Prince of Wales.
18.France (ancient) and England (quarterly).

The vault of the choir is of wood, like that of the nave; it is an imitation of the vault destroyed by the fire of 1829. It is covered with a network of ribs that obscure the main structural lines of the vaulting.

The aisles of the choir are of much the same size, design, and proportion as those of the nave. Their vault is of stone. The windows are filled with tracery of an unusual transitional character, and altogether more beautiful and interesting than that of the clerestory. They are divided into three lights, each terminating in a very obtuse arch. Above these arches are three others, also obtuse and hardly pointed. Short mullions run from the points of the lower arches to the points of the upper. Above the upper arches are three irregular-shaped openings, arranged pyramidally, the two lower being quatrefoiled, the upper sexfoiled. The whole is a curious mixture of vertical and flowing lines. They represent a design, as it were, of which the tracery is arrested half-way in its process of stiffening from the curved lines of the Decorated style to the straight of the Perpendicular. Here, as in the clerestory, the mouldings are delicately varied. The central shafts alone of the mullions have capitals. On each side of every window are three shafts, all with capitals.