Originally designed by F. X. Zettler of the House of Littler, Royal Bavarian Institute in Munich, Germany, and installed in 1908, the windows in the body of the Cathedral were completely rebuilt in 1992 by Rohlf Studios of New York. The windows on the west side (from back to front) portray the Joyful Mysteries of the Rosary (The Annunciation, The Visitation, The Nativity, The Presentation of Jesus, and the Finding of the Child Jesus in the Temple). The last of these is portrayed in the large west transept window, at the top of which is a scene of the woman, reputed to be St. Mary Magdalene, washing the feet of Jesus. Represented around this scene are (clockwise form the top) St. Gregory, St. Matthew, St. Jerome, St. Mark, St. Augustine, St. Luke, St. Ambrose, and St. John.
The windows on the east side (from front to back), beginning with the large east transept window, depict the Glorious Mysteries of the Rosary (The Resurrection, The Ascension, The Descent of the Holy Spirit, The Assumption of Mary, and The Crowning of Mary as Queen of Heaven). The Resurrection window also contains a medallion of Christ appearing to St. Mary Magdalen. Around this scene are (clockwise from the top) St. Farancis de Sales, St. Agnes, St. Stephen, St, Ignatius, St. Francis of Assisi, St. Bernard, St. Vincent de Paul, and St. Monica.
The two windows in the Blessed Sacrament chapel were designed by George W. Sotter of Pittsburgh in 1918 and display images of the twelve apostles. These windows exhibit a distinctly different style of stained glass from that in the body of the church. At the rear of the Cathedral above the organ is the great Rose Window depicting St. Cecilia, patroness of music, surrounded by angels with musical instruments.
