This window contains a number of shields of arms. Some of these including the arms of John Alcock (left) who was a fifteenth bishop of Ely are thought to have come from the east window of the Lady chapel. Other of the shields were given by a parishioner in the nineteenth century and are thought to come from Winchester. At the top of the window are fifteenth century canopy tops and at the base border pieces incorporating crowns and lozenges.

The St Thomas Window

Reflecting in its iconography its location above the altar of St Thomas the Martyr, is the St Thomas window. The left-hand lights portray the incredulity of St Thomas Apostle. We see the moment where doubting Thomas has plunged his hand into the Lord's wounded side, and at that moment recognises the risen Saviour: 'My Lord and my God'. To the right is a standing figure of an archbishop, vested in pallium and holding a cross staff. Despite the location of All Saints in York which had its own archbishop saint, William, this is probably intended to be the more popular St Thomas of Canterbury, the dedicatee of the altar below - thereby completing the St Thomas imagery. This is probably the window which Reginald Bawtrie, a city merchant, left one hundred shillings to complete in 1429. The window originally included a kneeling image of Bawtrie and of his uncle, Sir John Bawtrie. These survive at the bottom of the next window, where Sir John (a member of the Minster clergy) is shown reading from a book inscribed with texts that invoke St Cecilia and St Lucy to pray for him.

Corporal Acts of Mercy Window

The western window in the chapel, the Corporal Acts of Mercy window, was formerly in the westernmost window opening of the north wall. It may have been given by, or erected as a memorial to Nicholas Blackburn senior (father of Nicholas junior) who was a merchant and mayor of York. Six of the seven corporal (bodily) acts of mercy are shown. These are from top to bottom and left to right: feeding the hungry, giving drink to the thirsty, offering hospitality to strangers, clothing the naked, visiting the sick and relieving those in prison. The final act of burying the dead is omitted. The bearded man, who in every panel is performing the 'works', is perhaps Nicholas Blackburn himself. The panels are set within fine contemporary canopywork, notice the angels who sit high up peering over the parapet.

Pricke of Conscience Window

The iconography of the next window is unique in European art. It is based on an anonymous Middle English poem called the Pricke of Conscience. The text of the Pricke of Conscience was concerned with the final fifteen days of the world. The window reads from bottom left to top right with each of the final days given a separate panel with a Middle English text that paraphrases the poem. The first nine panels are concerned with the physical destruction of the earth. This begins with the seas rising and falling and giving up monsters that 'make a roaring that is hideous to mans hearing.' Then follows the destruction of buildings by an earthquake (see the new-built spire of All Saints falling), and the burning of all physical matter. The last panels illustrate the fate of frightened mankind, and the end of all things. Men hide in holes, emerging only to pray. Finally on the fourteenth day 'all that lives then shall die, both children, men and women.' The end of things comes, the stars fall from the sky, the bones of the dead rise, and finally the 'the world burns on every side'. As its name suggest the window is intended to be a moralistic call to repentance, so as a reminder of this, in the quatrefoil tracery lights at the top of the window, are two panels that show redeemed souls being let into heaven by St Peter and the dammed being taken to hell by demons. It is thought that members of the Henryson and Hessle families paid for this window. Both families, related by marriage, were among the freemen, who were the urban elite of medieval York. The kneeling figures of the families at the base of the window are particularly expressive and seem to look on in horror at the events going on in the panels above.

Joys of the Virgin Window

The mid-14th century glass in the east window of the chapel was formerly located in the east window of the chancel. It was moved and restored in the 1840s by Wailes of Newcastle. The iconography is that of the 'Joys of the Virgin', a summary of the major events in the Virgin Mary's life. The main panels at the bottom of the window are from left to right: the Annunciation, the Nativity, and Our Lord's Resurrection. The panels above portray the Adoration of the Magi, The Crucifixion and our Lady's Coronation as Queen of Heaven. The panels are set beneath elaborate canopies on a ground of trailing foliage, reminiscent of the glass produced by Robert Ketalbarn in the 1330s for the nave of York Minster.

Blackburn Window

The glass in the east window behind the high altar, The Blackburn window, was originally positioned in the choir of our Lady where the Corporal Acts window is now located. The main figures are from left to right: St John the Baptist, St Anne teaching the Virgin to read and St Christopher. The figures are set under canopies with figures of prophets in the borders. A technique called backpainting, which involves painting details on two sides of the glass is used to good effect on the wimple of St Anne and the water surrounding the feet of St Christopher - giving a soft three-dimensional feel to the glass.

The imagery reflects the spiritual pre-occupations of the Blackburn family, who gave the window in the 1420s. The head of the family, Nicholas Blackburn senior (who also gave the Corporal Acts of Mercy window) had a particular fondness for St Anne and founded a chantry in the chapel of St Anne on Fossbridge, which he adorned with his best chalice and best vestment. In 1416 he gave £10 to Durham cathedral to erect a statue in the shrine of St Cuthbert, either to St Anne, St Christopher or St John the Baptist - precisely the same combination of saints that we see in this window. Nicholas senior and his son Nicholas junior (who is buried close by) and their respective wives (both called Margaret) are shown kneeling at the bottom of the window on either side of the Holy Trinity. Nicholas senior is dressed in armour with a heraldic surcoat, an odd portrayal of a merchant that probably reflects his brief status as Admiral of the Northern Fleet in 1406-1407.

Fourteenth Century Window

The east window of the aisle was heavily restored in 1844 and little medieval glass now remains. Of the 14th century are the figures of our Lady and St John that flank the cross, and the kneeling figures below. The most notable feature of the window are the six 14th-century roundels at the top of the lights and in the tracery. These are decorated with angels or drolleries, i.e. hybrid creatures, playing musical instruments.

St Michael and St John Window

The eastern window in the south wall, the St Michael and St John window, was reconstructed in 1965 from fragments scattered around the church. The two standing figures are of St Michael (left) and St John the Evangelist (right). Very little is left of the image of St Michael, who is shown in full plate armour slaying a blue dragon. The figure of St John Evangelist, who is holding a palm and his eagle symbol, is better preserved. This window was probably paid for by James Baguley, a rector who died 1441 and four of his parishioners, including Robert Chapman and his wife. Sir James, the Chapmans and a further couple are kneeling at the base of the window.

Orders of Angels Window

The next window was reconstructed from fragments in 1965 following the discovery of a 17th century drawing by Henry Johnston of the window in a complete state. The iconography is that of the Nine Orders of Angels. A representative angel of each order leads a procession of mortals of the appropriate rank in medieval society. From top left to bottom right: the figure representing the Seraphim leads a group of top-level clerics, a Cherubim leads a group of clerks and scholars, while the figure that represents the Thrones leads members of the medieval legal profession. The figure representing the Dominations leads a group including two kings, a pope and an emperor, that representing Principalities leads a group of noblemen, while Powers are represented by an armoured angel who leads a group of priests. The figures that represent the Virtues, Archangels and Angels, are leading groups of average members of medieval York society. First are the middle-aged Burgesses, men like Nicholas Blackburn, who are accompanied by their wives in elaborate headresses. Working men and women are also shown: a labourer with a spade, a North Street tanner with his tools, a woman with a basket and a man holding up a pair of spectacles to his eyes. Perhaps they represent a group of parishioners who paid for the window.

St James, Our Lady and the Miraculous Mass Window

The first of the main figures in the next window (sVI) is St James, dressed in the garb of a pilgrim to his own shrine at Compestela. Next to him is our Lady crowned as Queen of Heaven and holding the Blessed Infant, and Christ appearing on the altar to an archbishop celebrating mass, perhaps St Martin or more likely St Gregory the Great. Robert Colynson (whose brass we have just seen in this aisle), asked in his will of 1450 for a priest to sing a daily trental of St Gregory in the church for the space of three years, so perhaps he paid for the image of St Gregory in the window. The borders of the window incorporate angels playing instruments and the bottom panel contain fragments of lost glazing from other parts of the church. The major fragments include: the head of a bearded man in chainmail and helmet, two figures of prophets and a circular inscribed border to a heraldic device. There are also portions of canopies, inscriptions, heraldic devices and a merchant's mark.

West window

The west window, below the tower, contains panels made up of fragments displaced from other parts of the building. The fragments include some late enamel work, including part of the seventeenth century royal arms, as well as fifteenth century heads, canopy elements and parts of inscriptions. The panels were put here when the church was restored in 1977.