Yesterday evening, Pope Francis prayed at the Basilica of Santa Maria Maggiore for the success of his trip to Africa, which begins today. He has a particular attachment to the church – this visit is his 27th since the beginning of his papacy.

Francis will be glad to leave behind the "Vatileaks" row that has seen journalists and officials put on trial for releasing information about a dysfunctional Vatican rife with financial mismanagement. However, the problems – and the opportunities – of the continent to which he is travelling are enough to put such local difficulties entirely in the shade.

The tour starts in Kenya and Uganda, which have both seen Islamist militant attacks, before he travels to the Central African Republic, a nation torn by Muslim-Christian strife. He will land in Nairobi this afternoon.

In a pre-trip message to the people of Kenya and Uganda the pope said: "We are living at a time when religious believers, and persons of good will everywhere, are called to foster mutual understanding and respect, and to support each other as members of our one human family. For all of us are God's children."

In a message to the CAR he said: "Your dear country has for too long been affected by a violent situation and by insecurity of which many of you have been innocent victims. The goal of my visit is, above all, to bring you, in the name of Christ, the comfort of consolation and hope. I hope with all my heart that my visit may contribute, in one way or another, to alleviate your wounds and to favour conditions for a better, more serene future for Central Africa and all its inhabitants."

"I am going with joy to Kenya, Uganda and the brothers of the Central African Republic," he told reporters aboard his flight to Nairobi. "Let's hope this trip brings better fruit, both spiritual and material."

Millions of Christians – Catholics and others – are expected to turn out in welcome and for public celebrations of Mass, presenting a challenge for national security forces to keep the pontiff safe and control the huge crowds.

Africa's Catholic Church is growing fast with an estimated 200 million adherents in 2012, a figure expected to reach half a billion in 2050. In Kenya, about 30 per cent of the 45 million population are baptised Catholics, including President Uhuru Kenyatta.

The size and rapid growth of the Church there present their own problems, with shortages of priests in some areas and a willingness to question orthodox teaching on issues such as the marriage of clergy. The harsh tone adopted by some Church leaders on homosexuality also jars with Pope Francis' warmer and more welcoming approach. 

"We are ready to receive him," Kenya's inspector general of police, Joseph Boinnet, told reporters. "Security arrangements have been put in place, right from arrival."

He did not say how many police would be deployed in the capital for the visit, which includes Mass at the University of Nairobi on Thursday, now declared a national holiday. Kenyan media has said at least 10,000 officers would be involved.

Kenya has been targeted by a spate of attacks by Somalia's Islamist group al Shabaab in the past two years that have killed hundreds of people. In 2013, an assault by al Shabaab gunmen on a Nairobi shopping mall killed 67 people.

Francis will also seek to heal ethnic rifts that have long plagued Kenya.

"Pope Francis' visit to Kenya will be focused on inclusivity and reconciliation in relation to ethnic and religious tolerance, peace and stability," Kenyan presidential spokesman Manoah Esipisu said.

The pope visits the Nairobi headquarters of the United Nations on Thursday and is expected to address climate issues.

In Uganda, where police said they would deploy 12,000 officers for the visit, the pope holds Mass on Saturday and then addresses young people on a continent that has a big youth belt.

Potentially the most hazardous stop of his trip is the third leg to the Central African Republic. Dozens of people have been killed there since September in violence between Muslim Seleka rebels and Christian anti-balaka militias.

His schedule in Bangui, the capital, includes a visit to a mosque in one of the most dangerous districts. French officials have hinted heavily that the Vatican should consider scrapping the Bangui leg of his trip or at least scaling it back.

The country has been plagued with violence in recent years, including gender-based violence. In a report just released by Christian relief and development agency Tearfund, To Make Our Voices Heard: Listening to survivors of sexual violence in Central African Republic, survivors describe their experiences of rape, gang-rape and other atrocities, as well as the stigma they have suffered from within their own communities and families as a result of the shame associated with sexual assault.

The report includes a call to Christian and Muslim faith leaders to work together to show leadership and speak out against the negative values, behaviours and attitudes which sexual and gender-based violence are rooted in, including where faith teachings have justified or condoned these.

It also calls on leaders to support survivors and lead by example to confront the stigma survivors are facing.

Speaking about the role of faith leaders, one survivor explained: "They have a responsibility to bring the issue to the attention of the political leaders to ensure the population respects human life, because human life is sacred."

Additional reporting by Reuters.