Below the windows runs an arcade of very simple panelling, four divisions to each window, and two trefoiled arches in each division. There is also panelling of the same character on each side of the vaulting shafts between the windows. The windows of the eastern bays are more sharply pointed than the others. The vaulting shafts of the aisles have capitals of carved foliage and wings of leafage on a level with the top of the arcade below the windows. The windows next to the east end have only two lights.

The eastern transepts stand between the four western and the four eastern bays. They mark the position of the eastern transepts and towers in Roger's Norman choir, and are of rather unusual design. They are of only one bay in width, and do not extend beyond the aisle walls. They therefore represent a bay of the choir, of which the clerestory and triforium are removed, and the aisle roof is raised to the height of the roof of the choir itself. Both outside and inside their effect is magnificent. Their north and south walls are filled with enormous windows, containing splendid glass. Of these windows, that on the north contains scenes from the life of St. William, and is known as the St. William window; that on the south, scenes from the life of St. Cuthbert, and is known as the St. Cuthbert window. Both have had their mullions recently restored.

These windows are divided into five lights, and are crossed by three transoms. Below these transoms, in each light, are cinquefoiled arches. The upper lights closely resemble those of the clerestory in design, and are of the same size. The main arch in these transepts remains, and is of the same character as that of the other main arches. Above it in each case is a gallery with panelled openings. Above the main arch, on each side of the transept openings, are thick clusters of shafts. The lower part of the windows has double tracery, like the great east window, and the east windows in the Chapel of Nine Altars at Durham, the inner tracery consisting of open lights about a foot off the actual tracery, containing the glass, and of exactly the same design. On each side of the windows are five canopies and brackets. The arches east and west of the transepts and opening into the aisles are of the same character as those opening into the choir. Above them are windows of the same size and design as those of the clerestory.

In the spandrels of the arches are coats of arms as follow:—

North Transept—East Side.

1. A chief, three chevronelles interlaced in base—Fitz-Hugh.
2. A bend, a label of three points—Scrope of Masham.

North Side.

1. Three escallopes—Dacres.
2. A fess between six cross crosslets—Beauchamp.

West Side.

1. On a saltire, a martlet—Neville.
2. A bend—Scrope of Masham.