The Holy See said the pontiff told Bush he would like to see a "regional and negotiated" solution to conflicts in the Middle East.
The U.S. president is also due to hold talks with Italian Prime Minister Romano Prodi on issues such as Afghanistan, Iran, and Iraq.
Tens of thousands of protesters have gathered in Rome to protest the Iraq war and U.S. foreign policy.
Italy, a key U.S. ally that hosts several NATO facilities, has 2,000 soldiers in Afghanistan and plays a pivotal role in Mediterranean diplomacy -- from Lebanon to the Holy Land.
In recent weeks, there has been speculation that Italy could withdraw its noncombat NATO forces in Afghanistan, as Communists in Prime Minister Romano Prodi’s ruling coalition oppose the military effort there.
Prodi already pulled Italy's troops out of Iraq in 2006.
But RFE/RL Rome correspondent Ahmad Rafat says Bush needn’t worry about that happening with Italy’s Afghan troops.
"As I understand it, they [won’t] speak that much about Afghanistan because Italy has guaranteed that it will stay," Rafat said. "At the same time, they have said that they are not going to change the role of [Italian] soldiers in Afghanistan. That means that they are not going to take part in attacks against the Taliban."
Rafat says Bush and Prodi will focus on Iran and Syria.
Meanwhile, a massive security lockdown has descended on the Eternal City, as thousands of mostly left-wing protesters gear up to rally against Bush’s visit.
Rome resident Umberto Zani told Reuters near the famous Trevi Fountain in central Rome that "Everything is shut down in Rome -- there is a massive security block. Fortunately, most people knew this and have stayed home."
Police with sniffer dogs were deployed at Rome's central station before the first trains carrying demonstrators arrived. Thousands of military police also took up position around the key areas of the city to try and ensure that the protests remain peaceful.
(with agency reports)