Today, traces of the original Norman edifice include part of the transept, the two towers and the three semicircular apses, composed of large lava stones, most of them recovered from imperial Roman buildings.

The main door, in wood, has 32 sculpted plaques with episodes of the life and martyrdom of Saint Agatha, papal coats of arms and symbols of Christianity.

In the southern aisle are the baptistery and, at the first altar, a canvas of Saint Febronia of Nisibis by Borremans facing, on a pilaster, the tomb of the composer Vincenzo Bellini.

The apse dates back to the original 12th-century construction: it features a medieval mullioned window and a late-16th-century choir by the Neapolitan artist Scipione di Guido.

It houses the tombs of members of the Aragonese branch of Sicily, including Kings Frederick III and Louis, John of Randazzo, and Constance.