In May-June 2005 the first stratigraphic excavations were undertaken on the ruins of the church of S. Francesco. Two years earlier the first investigation on the summit of Monte S. Francesco had surveyed and documented the structures of this ancient upland settlement, which emerged from the undergrowth, through the positioning of a series of fixed topographic and altimetrical benchmarks. The site, whose typology was clearly that of an early medieval castrum – as well as its particular toponym “in pertica” which would indicate the presence of a Lombard cemetery – seems to have been constructed for the defence of the ancient pilgrim route leading to the ancient incastellated Marian sanctuary of the Madonna del Monte. Subsequently, the monastery was built over the ruins of the military garrison, at the time of the beginning of the Franciscan movement in the territory of Varese. This phenomenon had an illustrious precedent, although of earlier date, in the Benedictine convent at Torba. The potential state of preservation of the stratigraphical deposit, due to the early abandonment of the monastery during the 16th century will be of great importance for this research.