1. St. Peter’s Basilica (Vatican City)
The heart of the Catholic Religion. This sacred site is above Vatican Necropolis a Roman burial ground with tombs from the 1st-4th centuries and even above the tomb of St. Peter.
2. St. John Lateran (Archbasilica of the Most Holy Savior)
The Cathedral that is the Basilica of the Diocese of Rome and serves as the seat to the pope. Since it is the "Mother of All Churches", it is formally the only church called an archbasilica. It is the Church that has the most connections to the Holy See that is outside the Vatican.
3. Holy Stairs (Scala Sancta)
The believed to be same steps that Jesus walked before he went on trial with Pontius Pilate. It consists of 28 marble stairs that were brought to Rome by St. Helena. Most people walk up on their knees as a sign of humility to Christ.
4. Catacombs of St. Callixtus
Created in the 2nd century by the future Pope Callixtus I, this serves as the final resting place to 9 popes and during the Roman Persecution years, it was used a safe spot to celebrate Mass.
5. The Mamertine Prison (Carcer Tullianum)
This is the same prison used by the Roman Empire to keep St. Peter and St. Paul before they were executed for Christ. On top of the two greatest apostles being kept there, it is one of the oldest prisons in the world. When you go, make sure you look for the spring that St. Peter used to baptize his guards. This is hardly ever crowded so you absolutly need to see it.