The frescoes in the chapel

They very well could have been authentic to the location where they filmed.

I stayed at a renovated monastery in Tuscany and the dining hall had frescoes the length of it.

Didn't take long to find your answer. Google is your friend.

"The actual Italian locations include the village, which is Pienza in Tuscany, and the chapel where Hana (Juliette Binoche) studies the frescoes. This is the 13th century Bacci Chapel in the Basilica of San Francesco at Arezzo, also in Tuscany. The frescoes, painted between 1453 and 1466 by Piero Della Francesca, have recently been restored. Reservations are required to view them, and, no, you can’t light flares or dangle from the ceiling."

"A Tuscan monastery (Sant 'Anna in Camprena) becomes a focal point within the film where the English patient reveals a serious of flashbacks when employed as a map maker charting the Sahara Desert in the 1930s.

They then moved on to Viareggio, a coastal resort town near Pisa, to create the emergency field hospital triage tent."

"The old ‘Shepheard’s Hotel, Cairo’ – the wartime watering hole for explorers, diplomats and spies which was destroyed in the fifties – is not Egypt either. Nor Tunisia. Surprisingly, it’s the Grand Hotel des Bains, Lungomare Marconi 41 on the Lido in Venice, the setting for Luchino Visconti’s Death in Venice."

http://www.movie-locations.com/movies/e/engpatient.html#.WEJWHneZORs