The choir, of three bays, is the work of Bishop Hotham. The last six bays are the work of Bishop Northwold, and form the presbytery. In the present arrangement seven of these nine bays form the ritual choir, and two form the retro-choir. The difference in date between the presbytery and choir may be roughly taken as very nearly a hundred years. The former had been begun in 1240; the latter was nearly finished in 1340. In the juxtaposition of these two magnificent specimens of the Early English and Decorated periods of architecture there is an opportunity of comparison which on such a scale occurs nowhere else. It is to be remembered that in neither case is the treatment of the upper part quite in accordance with the usual practice of the period. When the presbytery was being built there were still standing east of the central tower the four original bays of the Norman choir. These, it may be assumed, were very similar in character to those in the nave. There would, beyond question, have been in each bay large triforium arches, each with a couple of subordinate arches; and a single window in the clerestory with a blank arch on each side. Bishop Northwold's work was purposely made to correspond with these bays as far as Early English work could do so; and when after the fall of the tower it became necessary to rebuild the choir, Bishop Hotham in like manner made his Decorated work correspond with the Early English presbytery. The choir is, as would be expected, richer in detail as well as more elaborate in design; and it would be difficult to find in England anything to surpass the tracery of the clerestory windows and triforium arches, the beautiful cusped inner arches of the clerestory range, the open parapets at the base of the two stages, or the long corbels, covered with foliage, that support the vaulting shafts. In the choir the clerestory windows have four lights each; in the presbytery are triplets. The old colouring has been renewed throughout. On the north side of the choir the three bays are precisely alike; but on the south there is a variation in the tracery of the western triforium arch. There are also shields of arms (of the See of Ely and of Bishop Hotham) in the spandrels of the triforium and arch below; and the shaft between this arch and the next is enlarged at the top into a base for a statue (probably of S. Etheldreda); while level with the string above is a very fine large canopy (called by the work-men "the table"), which is like nothing else in the cathedral. The clerestory windows also on the south have different tracery.
The difference between the two styles of architecture is well marked in the groining of the roof, the Decorated portion being much more elaborate. Some of the bosses are very remarkable: one has S. Etheldreda with pastoral staff; one has the coronation of the Virgin Mary; one has the foundress bearing the model of a church, in which (as Dean Stubbs has pointed out) both arms of the western transept are represented, so that it is a fair inference that at the time this roof was constructed the whole of the western transept was standing.
Between the choir and presbytery there rise the massive Norman piers built as the entrance to the apse; and these are the only remains of the Norman church east of the octagon. Since the careful examination of the foundations here, made by Professor Willis in 1850, it is not thought certain that the apse was actually built. The foundations of the apse were very manifest, and the design did not include a passage round it; but there was also clear evidence that the apsidal foundation was altered into a straight wall of the same thickness, and the probability is that before the apse was built "it was resolved to convert it into a square-ended presbytery, such as we now see at Oxford Cathedral and St. Cross."[6]