St. Mary's 17 stained glass windows are truly an outstanding work of art. The jewel-like colors of these windows give the church a beautiful setting in which to worship... to hear God's Word, to celebrate His sacraments, and to offer him praises. The windows in the church depict the history of salvation starting with the creation of the universe through to the end of time. The ones on the west or Epistle side of the church deal with God's activities in regards to the Hebrew people, the historical drama set forth in the Old Testament. Those on the east or Gospel side focus on the coming of Jesus, centered in His life, death, and resurrection, and on the church today.
The Clerestory windows, found to the left of the altar, form a colorful pattern symbolizing the changing colors of the liturgical or church year. They form a harmonizing link to the rest of the church by admitting light through their bright and warm symmetrical patterns.
Additional stained glass windows were later added to the foyer rooms at the entrance of the church. Because of a light placed outside, the circular altar window depicting the body and blood of Christ is the only one at night whose radiance can be seen in an otherwise dark church.