Minard Lafever, designer of the Church in 1846, turned to William J. Bolton to craft stained glass windows that would complement the unique church. Bolton, the first artist in America to work in stained glass, was assisted by his brother John. The two had a studio in New York and produced the magnificent windows of St. Ann and the Holy Trinity in Brooklyn. For the simple lines of the Church of the Holy Apostles, they broke from their usual grandiose Old-World style reminiscent of the windows of Chartes, Westminster Abbey, and Tewkesbury. Instead, they opted for the clean light lines of the Tuscan order.
The windows are the jewels of the Church. They feature simple, sepia-toned round panes (occuli) that depict scenes from the Bible. These are surrounded by stylized panels of geometric and floral glass. Tradition holds that the Bible scenes were copies from illustrations in the Bolton family Bible. However, they do bear a resemblance to tapestries by Raphael in the Vatican.
Regardless of their origin, the windows must have been special to the Boltons, for these are the only ones of this design that the Boltons created while in the United States.
In 1854, when an extension was added to the Church, contractors were able to match the brick and extend the vaulting on the addition, but extrapolating the window design hit a snag: The Boltons had returned to England to take Holy Orders.
The firm of Sharp & Steel were retained for the four windows in the addition. Although the firm based its plan on Bolton designs, slight differences in style can be seen.