The Uganda Martyrs Shrine Namugongo has three permanent altars,
1. Basilica altar which stands at the center of the basilica, and at the exact spot where St. Charles Lwanga was burnt alive. Below this mahogany wood altar of an Italian design is a red light that symbolizes martyrdom and a glass containing a first class relic (bone) of St. Charles Lwanga.
2. Marian grotto altar permanently fixed in the grotto of Mother Mary Queen of the Martyrs. This terrazzo altar stands next to a demonstration of how St. Charles Lwanga was martyred.
3. Martyrs Lake altar which is mainly used for the Uganda Martyrs Day Celebration and other special celebrations held at the lakeside. This is a circular concrete pedestal supported by gig poles with a roof inspired by the African hut and a triangular sharped dome made of grey wooden panel shingles.
It has three steel carved polls supporting the roof, with the inner surface of the roof made up of white columns and ceiling made of steel with a metallic cross atop. This 200 setter altar has its sacristy and washrooms in the basement.
The relics of Charles Lwanga are some of the two Uganda Martyrs relics that were recovered.
A portion of Charles’ relics (a bone) is now kept inside the Uganda Martyrs’ Basilica in a glass attached to the basilica altar. It is open for public veneration and viewing to all pilgrims at all times.