The existing church was built by Pope Honorius I in the 7th century, and largely retains its original structure, despite many changes to the decoration.

The large basilica decayed during the decline of Rome, and was replaced in the 7th century by the present much smaller church, commissioned by Pope Honorius I.

On a gold ground, a central standing figure of Agnes in the costume of a Byzantine empress is flanked by Honorius, offering a model of the building, and another pope, whose identity is uncertain.

The church was also built with a separate upper gallery for women (matronaeum), similar to that of San Lorenzo fuori le mura.

[4] The church is the topic of Canadian author and anthropologist Margaret Visser's book The Geometry of Love, published in 2000, which describes it in exhaustive detail and discusses aspects of history, theology, architecture, symbolism and the emotional and aesthetic effects of visiting the church.