To the west of the Vieux Port lies Abbaye St-Victor, the birthplace of Christianity in Marseille, built on a 3rd-century-BC necropolis. It's €2 to visit the crypts, with guided tours available from 4pm to 6pm on Tuesdays as well as on the first Saturday of the month (or download an audio tour from www.saintvictor.net – click "Visit").
