While the Stations of the Cross serve as a reminder of the passion and death of Jesus, the stained glass windows found along the walls of the nave and transepts call to mind the Mysteries of the Rosary. These twenty mysteries are significant events in the life of Jesus and Mary. They are a source of catechesis and devotion.

In the transepts, the windows depict the Joyful Mysteries and the Luminous Mysteries.

The east transept contains the Joyful Mysteries: The Annunciation of Gabriel to Mary, The Visitation of Mary to Elizabeth, The Nativity of Christ, The Presentation in the Temple and Finding Jesus in the Temple of Jerusalem.

The Luminous Mysteries are in the west transept. Pope John Paul II gave them to the church. The mysteries depicted are The Baptism of Jesus in the Jordan River, the Wedding at Cana, The Proclamation of the Kingdom of God, The Transfiguration of Jesus and The Last Supper.

Found among the west transept windows are the coat of arms for Pope John Paul II and Pope Benedict XVI. Another window has the coat of arms for Archbishop Wilton D. Gregory, Archbishop of Atlanta, who dedicated the church on November 4, 2005. The symbol for the Year of the Eucharist (2004-2005) is included to commemorate the ecclesial year the church was dedicated.

Windows in the nave depict the Sorrowful Mysteries and the Glorious Mysteries.

The Sorrowful Mysteries include the following events: The Agony of Jesus in the Garden, Jesus Scourged at the Pillar, Jesus Crowned with Thorns, Jesus Carrying His Cross and the Crucifixion of Jesus.

The Glorious Mysteries are The Resurrection of Jesus, The Ascension of Jesus, The Descent of the Holy Spirit at Pentecost, The Assumption of Mary into Heaven and The Coronation of Mary as Queen of Heaven and Earth.