The 12 round stained glass windows in the clerestory were made by the W.H. Carse Co. of Chicago in 1860 and are the oldest stained glass in the city.

The original windows in the nave of the church were purchased in 1859 at a cost of $1,004.00.  This money was raised by a host of volunteers who canvassed the parish for donations.  In 1907, to celebrate the Golden Jubilee of the parish, the original windows were replaced with the current windows.  These windows were made Von Gerichten Art Glass Co. of Columbus, Ohio.

The following descriptions of the stained glass windows are taken from the book, "Holy Family Parish: Priests and People," written by Br. Thomas M. Mulkerins, S.J. and published in 1923. 

The eight principal windows, along the nave of the church, present scenes from the lives of Jesuit saints.

The first, on the west side, represents the beginning of the Society of Jesus, when St. Ignatius and his companions bound themselves, by vow, to undertake the great work planned by St. Ignatius.  It is called the "Window of the First Vows."

The second depicts the death of St. Francis Xavier on a desert island, with no one near him but his faithful Japanese servant.

The third is a double panel, one of which shows St. Alphonsus in prayer, and the other the effect of that prayer, the baptism of an African slave by St. Peter Claver, whose work among the African slaves had been foretold by St. Alphonsus.The fourth window on the west side presents the Jesuit missionary.  Alone, on foot, with modesty and holiness of countenance, he is accompanied by angels.  

The first window on the east side of the nave contains images of St. Aloysius gathering youths around the shrine of Our Lady.  The scene is laid in the garden of a Jesuit Scholasticate, or House of Studies.  In the background is the building where he spent his days as a Jesuit student.  It is separated by a wallfrom the court where St. Alyosius, kneeling at the side of the altar, is directing three boys, who are placing flowers on the altar of the Virgin.

In the second window, is an incident in the life of St. Stanislaus Kostka.  While boarding with his brother, in the house of a Lutheran family, he was suddenly became ill.  His brother locked him is a room in an effort to deprive him of the consolation of his religion.  God knowing his longing to receive the Eucharist, sent St. Barbara to gratify his desire by a miraculous reception of the Sacrament.

Sts. John Berchmans and Francis Borgia are the subjects of the third window.  The former is kneeling with his book of Rules, his rosary, and his crucifix in his hands.  He was always faithful to duty, and his fidelity raised him to the altar.  St. Francis Borgia, while Duke of Gandia, resolved to forsake worldly ambition and pleasure after he had gazed at the dead face of Isabella the Beautiful.  It made him realize the emptiness emptiness of creatures and offer himself entirely to the servie of God.  He is pictured kneeling in prayer before the Blessed Sacrament, from which rays of light stream upon his face.

The fourth window shows Sts. Francis Regis and Francis de Hieronymo in the attitude characteristic of those, who by their own saintliness, have brought grace and salvation into the lives of those for whom they labored.