Visitors to the church are blessed with many colorful and unique stained-glass windows to contemplate. There is a large round window high on each end of the structure with the Holy Family on the east and the patron St. Thomas on the west to bookend the congregation with grace.
On the side walls are images of Jesus and the Saints; and high on the side-walls are smaller, nearly-square windows bearing symbols of the Church and liturgy. The windows were part of the original construction of the church and were thankfully refurbished in February 1975 as they had sustained some damage due to the elements over the years.
The round window of the patron, St. Thomas the Apostle, near the peak of the western façade, greets attendees, particularly at night since the image has been lighted from the inside since January 1983 at the direction of the pastor, Father Dermot Dwyer. The colorful window primarily of hues of blue, red and white depicts the famous utterance of faith by St. Thomas to Jesus in the Upper Room, as recorded in the Gospel of John, Chapter 20, verses 24-29. Thomas was not present the first time that Jesus appeared to His apostles in the Upper Room. Upon hearing of this, Thomas said that he would not believe that Jesus had appeared “Unless I see the mark of the nails in his hands and put my finger into the nail marks and put my hand into his side, I will not believe.” (John 20:25) One week later, Jesus again appeared to the apostles and Thomas was there. Jesus said to Thomas, “Put your finger here and see my hands, and bring your hand and put it into my side, and do not be unbelieving, but believe.” (John 20:27) Thomas responded with his famous utterance of faith and belief, “My Lord and my God!” (John 20:28) The inscription at the bottom of the window indicates that the window was donated by Daughter Marybelle O’Brien in memory of her parents, Mr. and Mrs. John F. O’Brien and their family.