In the interests of accurate history and to avoid misunderstandings about the Saracens who harassed Assisi, Tertiary Michael Giffin gives some evidence to show that these Saracens were resident in southern Italy, and were attacking Assisi to do the Emperor's bidding, not for religious reasons.

WHO DID CLARE REPEL?

by MICHAEL GIFFIN tssf

Clare repelled freelance Saracen soldiers in the army of the Holy Roman Emperor,

Frederick II, not Saracens who represented an Islamic threat. All Franciscans need

to be aware of this distinction lest we contribute to inter-faith misunderstanding.

Here are some references:

http://www.answers.com/topic/clare-of-assisi

Clare lived during a tumultuous period in Italian history, and in 1234 San

Damiano's walls were transgressed by soldiers in the army of the Holy Roman

emperor, Frederick II. Clare was ill in bed but reportedly rose and went to the

window with a ciborium, a chalice-like vessel that was used at the time to house

the Eucharist. She was said to have raised the ciborium at the soldiers—some of

them Saracen, or Muslim—who had mounted a ladder, and they fell over backwards

and fled.

http://www.therealpresence.org/eucharst/mir/english_pdf/Assisi.pdf

The History of Saint Clare, Virgin, tells of various miracles performed by Saint

Clare. There are episodes of multiplications of loaves and of bottles of oil that

appeared in the convent when there was none before. But Clare performed the

most famous of the miracles in 1240 on a Friday in September, in which she turned

away an attack by Saracen soldiers who had broken into the convent cloister by

showing them the Sacred Host.

[Note: the term used here is “Saracen soldiers” not “Islamic

soldiers”. The distinction is important. MG.]

http://www.deremilitari.org/resources/articles/saracen_archers.htm

During the first phase of their Southern Italian conquest, the Normans included

archers in their troops; but such usage seems to have been sporadic and simple …

According to Anna Commena, the archers that accompanied the Norman

expeditionary force in Epirus were just young striplings and decrepit old men,

recruited from every part of Southern Italy, and they did not have any knowledge

of handling a bow …

In early twelfth century Southern Italy, as in the rest of the Continent,

crossbowmen were being increasingly used in place of archers. But an important

exception to this was represented by the presence of Muslims, whose culture

contained a strong archery tradition, in the Norman-Swabian armies. The Normans,

soon after the conquest of Sicily was complete, began using Sicilian Saracen

mounted and foot archers as auxiliary troops …

Fredrick II reinforced the use of Saracens in Southern Italian armies. After having

put down the last of the rebellions in Sicily he deported to Lucera, in Puglia, the

most troublesome Saracens who had refused to convert. Here the Emperor founded

a flourishing Arab colony, which continued their traditions and customs for about a

century, as well as the right to practice their own religion.

http://en.wikipedia.org/wiki/History_of_Islam_in_southern_Italy

The Islamic conquest and rule of Sicily, Malta, and parts of southern Italy was a

process whose origin can be traced back through the general expansion of Islam

from the 7th century onwards. Though the Muslim presence was ephemeral on the

peninsula and limited mostly to semi-permanent soldier camps—the Emirate of Bari

existed for only twenty years or so—their rule over the island was effective from

902, but their complete rule of Sicily lasted only from 965 until 1061, though they

were not completely evicted until 1091.