Sheikh Mukhtar Robow, member of the Islamic Courts Union, said there was a "concrete possibility" that the murder of the nun was "a reprisal for the Pope's remarks on Islam". However, several humanitarian workers and Christian volunteers have been murdered by Islamic gunmen in Somalia, including Italian bishop Salvatore Colombo shot dead during celebrating mass in Mogadishu in 1989 , Graziella Fumagalli, an Italian medical doctor, killed in 1995 in the anti-TBC Center she was running ; Annalena Tonelli assassinated in 2003 in a unique relief center in Borama, after 33 years of service to the poorest , and Dick and Enid Eyeington in 2003.

In Iraq, the flags of Germany, Israel, and the United States, and Christian crosses and effigies of Pope Benedict were burned in Basra.

Iraq has one of the largest Christian minorities in the Middle East, where Assyrians number about one million. Since the Pope's comments, several churches have been bombed; however, many were being bombed since before the Pope's comments starting with the US invasion in 2003 in the power vacuum created by the fall of Saddam Hussein. A previously unknown Baghdad-based group, Kataab Ashbal Al Islam Al Salafi (Islamic Salafist Boy Scout Battalions)[Note 1] threatened to kill all Christians in Iraq if the Pope does not apologize to Muhammad within three days. Christian Leaders in Iraq have asked their parishioners not to leave their homes, after two Christians were stabbed and killed in Baghdad.

There have been reports of writing in church doors stating "If the Pope does not apologise, we will bomb all churches, kill more Christians and steal their property and money."

The Iraqi militia Jaish al-Mujahedin (Holy Warriors' Army) announced its intention to "destroy their cross in the heart of Rome… and to hit the Vatican."

Despite the Pope's comments dying down in the media, attacks on Assyrian Christians continued and on 9 October, Islamic extremist group kidnapped priest Paulos Iskander. The relatives of a Christian priest who was beheaded 3 days later in Mosul, have said that his Muslim captors had demanded his church condemn the pope's recent comments about Islam and pay a $350,000 ransom.

Another point of controversy, widely covered in Arab media, but much less so in Western media, was the Pope's assessment that sura (i.e. Chapter) 2 in the Qur'an, which includes the verse "There is no compulsion in religion", was "one of the suras of the early period, when Muhammad was still powerless and under threat", and that instructions "concerning holy war" had come later.

Many scholars of Islam have taken this as a classification of the sura as stemming from the earlier Meccan period and have shown the Pope to be mistaken by pointing out that Surah 2 was revealed in various stages and that this verse was revealed after Muhammad's hijra from Mecca, during his period of stay in Medina and hence is from the Medinan period which was the final stage of the revelation of the Qur'an when the Muslims were becoming numerous and increasingly powerful and safe from the immediate dangers that had overshadowed them for 13 years in Mecca. The scholars also point out that the Pope failed to mention that even if this verse was revealed when the Muslims were weak, they could have easily abrogated it with another verse which gave them permission to forcefully convert people once they finally conquered Mecca; this, however, did not happen..

In contrast to the Jyllands-Posten Muhammad cartoons controversy - which is now deemed a precursor to the controversy over the Pope's lecture[citation needed] - the media focus was not on the issues of free speech or injured religious sensitivities. Underlying the widely talked about question of whether or not the Pope should apologize, and whether or not his subsequent statements even constituted an apology, several competing and separate interpretations of his intentions have been proffered. These are, broadly and in no particular order: