The Great East window above the high Altar was erected in 1898 to commemorate the Diamond Jubilee of Queen Victoria, and is universally admired. The window was put in by subscription, and formerly there was a brass tablet on the North wall of the Chancel which recorded the names of the subscribers:-
The East window was given in 1897, the Victoria Diamond Jubilee Year by the following donors; Four principal lights with corresponding smaller ones by J. H. A. Whitley. Esq. of Ashton; one light by Edward H. Beaman Esq. of Southport; One light by Charles T. Street Esq. of Haydock Lodge; One light by Mary Owen, Arthur Hatton, and W. Hatton. Mr and Mrs. W. Painter gave £10 towards expenses.
The general subject of the window is the redemption of man, the subjects of the seven lights from left to right being:

1. The fall and expulsion from the Garden of Eden.
2. Abraham about to offer Isaac.
3. The agony of Gethsemane.
4. The Crucifixion.
5. The Resurrection-The Risen Christ appears to Mary.
6. His appearance to Thomas-"My Lord and my God.
7. The Ascension.

The figures in the top four lights are St Peter, St Thomas, St Oswald, and St Paul. The inclusion of St Oswald, is a reminder that the Church is a daughter Church of Winwick which is dedicated to St Oswald. The ten small lights below contain the figures of the rest of the Apostles, the order from left to right being:

St Matthew
St Andrew
St John
St James the Great
St Jam the Less
St Simon
St Bartholomew
St Jude
St Phillip
St Matthias

The window was competed for by a number of firms, and the successful design was submitted by A. L. Moore of London.
There are five other stained glass windows, all in the South Aisle. It appears that the subjects for all six windows were arranged in advance, and were to be in the following order from West to East:

The Nativity
The Presentation of Christ in the Temple.
Christ's Baptism by John
The Transfiguration of our Lord
The Resurrection
The Road to Emmaus

Three of these - Christ's Baptism, His Transfiguration, and Resurrection-were subsequently put in, but the original plan was later abandoned or forgotten, as the fourth window is not part of the scheme. This is the one nearest to the Vestry, dedicated to the memory of Ellen Billingham, died 11 March 1964. Appropriately, the subject is "Suffer little children to come unto me" as this window adjoins the present Baptistery.

The next window, moving West towards the back of the Church, represents in the centre light the Resurrection; in the East light are the two Mary's, and in the West light St Peter and St John. In the traceries above these main lights are the badges of the Bay's and Lancashire Hussars, and the words "Ad deiomnia gloriam" The window was erected by the Officers, non-commissioned officers, and men of the Lancashire Hussars, "In memory of their old comrade, Major Benjamin Relf, who died on March 5th 1897 aged 64 years."

St Thomas's is unusual in having a Boer War memorial, as the third window-The Transfiguration of our Lord-is "in memory of the men of the 32nd Company Imperial Yeomanry (Lancashire Hussars), who were killed in action or died in South Africa 1900-1901." They are named as:

Private Clarke Private Littler Private R. Collinge
Private H.Gerrard Private Frost Private R.Howard
Private A Ogden Seargent A. Owbridge Private Herrity
Private Fairclough Seargent S. Swan

The Lancashire Hussars were a Volunteer Yeomanry Unit raised in Bolton in 1798, when there were fears of a Napoleonic invasion. During the Boer War, volunteers from Yeomanry Units were sent to South Africa, formed into companies of the Imperial Yeomanry, and were used to patrol lines of communication especially railways, and to hunt down the Boer guerrillas and commandos. It should be remembered that more Soldiers died from diseases than bullets, enteric fever, typhoid and dysentery being the principal killers. The middle light of this Window shows Christ in Glory, flanked by Moses and Elijah in the two side lights.
The fourth window, depicting Christ’s baptism in the Jordan, is "to the Glory of God and in memory of James Watson, many years Sidesman of this Church, who died 9th April 1898 aged 45 years." The words "Behold the Lamb of God" are inscribed in the small traceries above the main lights.