Pope Francis on Thursday condemned the "brutal persecution" of minorities by Islamic State insurgents and said the joy of Christmas was marred by the suffering of children in the Middle East and around the world.

Tens of thousands of people flocked to St Peter's Square to hear the Argentine pope deliver his "Urbi et Orbi" (to the city and the world) blessing and message, marking the second Christmas since his election last year.

He condemned Islamic State fighters who have killed or displaced Shi'ite Muslims, Christians and others in Syria and Iraq who do not share the group's ideologies.

"I ask him, the savior of the world, to look upon our brothers and sisters in Iraq and Syria, who for too long now have suffered the effects of ongoing conflict, and who, together with those belonging to other ethnic and religious groups, are suffering a brutal persecution," he said.

Later he departed from his text and spoke emotionally of "children displaced due to war and persecution, abused and taken advantage of before our very eyes and our complicit silence."

"I think also of those infants massacred in bomb attacks, also those where the Son of God was born," he said, without elaborating. Again without elaborating, he spoke of "contemporary Herods," with blood on their hands.

He also spoke of "infants killed in the womb" condemning abortion as a product of "a culture that does not love life."

Speaking of the plight of refugees he asked that "indifference be changed into closeness and rejection into hospitality, so that all who now are suffering may receive the necessary humanitarian help to overcome the rigors of winter, return to their countries and live with dignity."

He appealed for an end to conflicts in African countries, urged dialogue between Israelis and Palestinians, condemned the attack by Taliban militants that killed more than 130 students in Pakistan last week, and thanked those helping the victims of the Ebola epidemic.

On Christmas eve, Francis made a surprise telephone call to comfort Christian refugees in a camp in Ankawa, Iraq. "You are like Jesus on Christmas night. There was no room for him either ..." he told them.