At the east end of the south aisle stands a marble life-size statue by Bailey of Thomas Fleming, who died in 1848, and a memorial tablet to the Rev. George Ogden, B.D., who died in 1706. The aisle is divided from the choir by a wooden screen; in the third bay from the east are iron gates leading into the choir. The retro-choir, about thirteen feet from east to west, runs between the back of the modern reredos behind the high altar and the beautiful mediaeval screen which stands beneath the arch at the entrance to the Lady Chapel. The Lady Chapel has modern fittings making it suitable for the celebration of Holy Communion when the congregation is small. In the south wall a piscina may be noticed, and on the north side of the altar stands a Renaissance font of grey-veined marble which was formerly in use in the nave. There are marble tablets in memory of various members of the Chetham family at the west ends of the north and south walls of the Lady Chapel.

On the west wall of the arch leading into the chapel may be seen the rebus of Sir John Huntington, the first warden and rebuilder of the church. On the north side is a man and dog hunting, on the south side two tuns of wine. This rebus is repeated in the roof of the choir. At the north-east corner of the north choir aisle may be seen a statue by Theed (1853) of Humphrey Chetham, the founder of the Hospital (i.e. school) and Library that bears his name. He sits, a roll in his right hand, with long hair and pointed beard, a ruff round his neck, and a long cloak which, falling open in front, shows doublet and slashed trunk hose. At the bottom of the pedestal sits one of the boys of the hospital school, pointing with his left hand to a book which he holds open in his right, on which we read the inscription: "He hath dispersed abroad, and given to the poor, and his righteousness remaineth for ever" (Ps. cxii. 9; Prayer-book version).

An old oak screen running under five arches of the arcading to the north side of the aisle separates the Derby Chapel from the aisle. This screen is of good design, but the workmanship is not so good as that of the other old screens in the church. Near the first pier, counting from the east, is the altar tomb of Hugh Birley, M.P. for Manchester, with a recumbent figure. Here also may be seen an old oak deed chest. About halfway down this aisle on the south side may be seen a small organ built by the celebrated Father Smith, dated 1680; this is of the finest tone and is still frequently used. It has one manual with seven stops and pedal with one stop.

Four steps lead from the outer nave aisle on the north side into the antechapel that stands to the west end, outside the entrance to the Derby Chapel.

This chapel is dedicated to St. John the Baptist. It was a private chantry built and endowed by the Stanley family, of which the Earls of Derby were members. Two of the family were closely connected with the church. One, James Stanley, Prebendary of St. Paul's, and archdeacon of Chester, held the office of warden from 1481-1485, and was succeeded by another James Stanley, whose tenure was longer, 1485-1509. He it was who began the building of the Derby Chapel. He became bishop of Ely, but when he died in 1515 his body was buried at Manchester, close by the screen of the Ely Chapel; but "for reasons which need not be mentioned here" his body was laid just by the wall, and the chapel was erected by his son according to his will over his grave, and called after the name of his diocese. This tomb still stands there, with its original brass and curiously inscribed epitaph, for which see hereafter.

The following description is copied from a MS in Chetham's Library.

"In the old or Christ's Church, Manchester, is a Chapell dedicated to S. John Baptist on the screen which separates it from the broad north aisle and over door leading from the aforesaid chapel into the aisle is an ancient coat of arms carv'd in wood, and three old brass inscriptions setting forth the founders of the chapell together with ye cause of its erection.