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Vatican Museum and Basilica best plan

We have devoted a full day to visiting the Vatican Museums, Sistine Chapel and Basilica. It is our first trip to Rome and we will be buying a guided tour of the Museums. I have read "Ron-in-Rome" but need clarification on the most efficient order of visiting. What is the preferred order of events? Is it, do the tour first then go to the Basilica, or go through the Basilica first, then head over to the pre-booked tour? Also what is the best bus to take from the Termini station?

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If the Vatican museum is open, go there first. You will arrive at the Sistine Chapel after walking through the museum. BTW, this is a world-class museum and has siderooms with wonderful art. There is a side-door exit from the Sistine Chapel (possibly labelled "for groups only") that leads into the basilica. Rick Steves recommends using this door. I have gone into the basilica this way. If you go to the basilica first, you will have a long hike out and around to the museum entrance. Choosing to visit the basilica first, you may want to take a lunch break somewhere in the area as you walk to the museum. I think there is a cafe in the museum. I don't know about buses, but it is common to take the Metro to a stop near the Vatican and walk about ten minutes to the museum or basilica. Just follow the crowds.