The Museum's paths (currently crossable nearly 12000 square metres) are organized in levels.
The level of the Piazza Duomo (level 4) leads to the monumental area with the church of Santissima Annunziata, the Old Sacristy, Palazzo Squarcialupi, the Chapel of Our Lady and the Chapel of the Mantle. From here you enter the Pellegrinaio and you can see the famous fifteenth-century fresco cycle, through a bright hall named Passeggio on which there are side rooms in past times used as hospital wards and at present days reused as exhibition spaces and museum areas. From the lower level (level 3) you enter the Corticella, an inside junction of Santa Maria's paths. This area gives access to the Fienile (medieval hay-loft): here the Fonte Gaia by Jacopo della Quercia is kept. In the same place there are the seats of two laical confraternitites: the Brotherhood of Saint Catherine of the Night and the Company of Saint Mary under the Vaults.
The Corticella, or little courtyard, gives access to the "tunnels" under Santa Maria della Scala (level 1) where is the current arrangement of the archaeological museum.