Politics and religion rarely mix well, especially in central Africa where the Catholic Church has become entangled in bitter ethnic politics and its clergy are accused of inciting hatred and orchestrating genocide.
A Rwandan bishop, Augustin Misago, is currently on trial for allegedly plotting the 1994 genocide in which over 500,000 Tutsis and moderate Hutus were murdered. If found guilty he faces the death penalty.
In eastern Congo an outspoken archbishop, Emmanuel Kataliko, has been expelled from his dioceses after clashing with the Rwandan authorities. They accuse him of inciting ethnic hatred against Tutsis; he says he is merely speaking out for human rights and justice.
And in Europe, Catholic orders are accused of harbouring priests and nuns on the run, Rwandan clergy wanted on genocide-related charges in their own country.
Relations between the Catholic Church and the Rwandan government have been fragile since the 1994 genocide, when churches were the scene of some of the worst massacres. Thousands of terrified civilians seeking sanctuary were slaughtered by Hutu extremists during the 100-day killing orgy.
While many religious died trying to prevent the attacks, others - particularly members of the hierarchy - have been accused of encouraging the massacre of Tutsis. Two priests have already been sentenced to death, while several other religious are in jail awaiting trial.
But the Rwandan church has protested its innocence. It says its priests and nuns could do nothing to prevent the genocide, and protests that those on trial are being unfairly scapegoated for the sins of a nation. "We have no apology to make for our role. We tried but people would not listen to us," said Archbishop Thaddee Ntihinyurwa of Kigali.
Relations between church and state now hinge on the trial of Bishop Augustin Misago, which is nearing judgment. The case has been mired in controversy from the start.
Bishop Misago's arrest last April came exactly one week after the Rwandan president at the time, Pasteur Bizimungu, accused him of ignoring persistent allegations of involvement in the genocide. Although he had not been arrested the bishop was "not above the law", the president said.
Bishop Misago was arrested and forced to don the pink uniform of a genocide suspect. In his opening statement last September, the bishop said his arrest had a "political stamp". He claimed that police investigations started only after his arrest, which was later denied by the authorities.
The Vatican called his jailing an act of "extreme gravity" which had "profoundly hurt" relations between Rwanda and the Holy See.
During the trial, state prosecutors charged Bishop Misago with leading three priests and 30 Tutsi students to their death, and conspiring with local authorities to orchestrate the killings.
Bishop Misago denied responsibility for the killings and said he did his best to protect those in his care. He said he met the authorities to organise the distribution of food and medicines, and did not know they were orchestrating the killings.
Allegations against Bishop Misago were first published by the human rights group, African Rights, in 1995. In recent months African Rights has accused European Catholic orders of sheltering other Rwandan priests and nuns accused of genocide-related crimes.
The organisation has collected accounts from 34 witnesses accusing Sister Gertrude Mukangango and Sister Julienne Kizito of encouraging the massacres. The nuns are currently living with the Benedictine order in Belgium.
Similar accusations have been levelled against Father Athanase Seromba now working under an assumed name in a parish in Florence, Italy. A former policeman told African Rights: "Father Seromba was firing at one of the church doors. I could see him clearly. He wasn't wearing a soutane. He was carrying an R4 rifle."
But however bad relations are in Rwanda, they are much worse in Congo where a Catholic archbishop is sitting on an ethnic powder keg that could explode at any time.
Rwandan-led rebels from the Congolese Rally for Democracy (RCD) expelled Archbishop Emmanuel Kataliko from his home diocese of Bukavu last month, claiming he had been encouraging ethnic hatred.
The expulsion was provoked by the archbishop's Christmas address, in which he condemned the "foreign powers" that were "pillaging" the resources of the Congo and terrorising its people. It was an unequivocal reference to the RCD, which is intensely unpopular with the local population.
The expulsion provoked a storm of protest and the archbishop has become the focus of resistance among local people. The Pope intervened personally, calling the case "a grave violation that painfully injures all Catholics".
But there are fears that the archbishop's comments have also fed local ethnic hostilities. In his speech he singled out "Congolese brothers" for collaborating with the rebels. This was seen as a reference to the Banyamulenge, an ethnically Tutsi tribe with its roots in Rwanda.
In the aftermath of the bishop's expulsion, alarming tracts circulated in Bukavu calling for the violent expulsion of all Tutsis from eastern Congo. Some made specific reference to the Banyamulenge.
"There are 1,000 reasons to complain about the RCD. But his speech carried no message of forgiveness or respect for others, and that is where it was dangerous," the director of one aid agency said.
In the archbishop's absence, this reporter met a group of seven senior priests from his diocese, of which three were Italian missionaries. They were uncompromising in their criticism of Rwanda and of all Tutsis.
The priests cast doubt on the figure of 500,000 Tutsis killed and advocated instead the double-genocide theory, that atrocities committed by Tutsis equalled those of the Hutu militia.
They claimed the Rwandan government manipulated international sympathy following the 1994 genocide to justify its presence in Congo, which they said was a "colonising" one.
With regard to the Banyamulenge, one priest said they were welcome in Congo, "but only if they take a correct attitude".
The Italian missionaries held some of the most trenchant views within the group.
Archbishop Kataliko's return to Bukavu is being negotiated. One Western diplomat said: "He will have the authority to either lead a process of reconciliation between Congolese, or to further fuel division and hatred."
Last week's papal visit to the Holy Land went some way towards healing long-festering wounds with the Jewish people. But in the Great Lakes region much reconciliation remains to be achieved, both within and outside the Catholic Church.
Last week a Belgian court ruled that the two nuns should be tried in Belgium. Legal experts have hailed the decision as a landmark precedent for the trial of genocide suspects sheltering in Western countries.