Scavi Tour at 12 PM....Vatican Museum/St. Peter's before/after?

Are you self-guiding? I'd say hit the Basilica before and the Museums after as the museums are reputed to be less busy in the afternoon. Basilica: arrive by 10:00 AM. You have to go through Security; Check your backpack if you have one as Scavi Tour does not allow. You don't want to have to go through the Security line twice so check your bags first thing. (You could also go to the Basilica on one of your other days if you have time and it is convenient) Scavi: arrive 11:45 AM (must present yourself 15 minutes in advance, but no more than that) Lunch break @ 13:30 (Scavi tour takes 90 minutes) Museums: 15:00 or thereabouts. Closes at 18:00, so gives you three hours. By the end of 3 hours you'll be exhausted anyway, so it's enough. :-) Best bet for lunch is to get away from the immediate area of the Vatican, at least by a few blocks. Sit down somewhere and REST between these events. It's a long but VERY interesting day!

I would do just the opposite. I would purchase early morning entry tickets for the museums and spend the morning there. You can take your time and exit in just enough time to be at the scavi office 15 minutes prior to your tour. Don't forget to check your bags or they won't let you on the tour.
After the tour I would visit the basilica. You exit into it so, to me, it makes more sense to do it this way, but you should choose whichever you're more comfortable with. Depending on when you leave the museums you could catch a bite to eat on the way to the scavi tour or just eat at the cafeteria inside the museums. donna

Thank you! We are self-guiding (as of right now ;-) ). We were leaning towards Museum, then Scavi tour, then Basilica. This is our last day in Rome, and I had hoped to do touring at the Vatican on another day, but with the 2 June holiday (Scavi closed on 2 June), that was not to be!

We did museum, then scavi, then basilica. A long day, to be sure, but you can go from the scavi straight into the basilica and avoid the line.