"Christianity reaches more people than healthcare," Stephen Waititi, a former church deacon and the medical director of Milmay Centre, an HIV/Aids clinic in Kampala, pointed out recently.

What the churches say matters: not just because of their reach, but because of their authority. The message from the pulpit shapes the climate. The role of the church in the HIV/Aids epidemic is central.

From the first recognition of the threat posed, above all, to the poor of the developing world, the churches have been at the forefront of the effort to provide care for the sick and to educate the healthy. The exception was the Christian evangelical movement, which by 2000 claimed not just the Ugandan president and his wife, Yoweri and Janet Museveni, but George W Bush, the president of the United States.

Jerry Falwell, then the leading US televangelist, called Aids "God's judgment on promiscuity", while senator Jesse Helms, a powerful Congressional ally of the evangelicals, argued against Aids funding for homosexuals because of their "deliberate, disgusting, revolting acts".

But, as Helen Epstein charts in her brilliant article in the New York Review of Books, the evangelical right soon saw that however morally reprehensible, HIV/Aids opened new avenues.

"It is true," wrote Ken Isaacs, of Samaritan's Purse, an evangelical charity run by Billy Graham's son, Franklin, "that when we choose to act outside of God's mandate for sexual purity, we should be prepared to deal with the consequences.

"However," he went on, "God calls Christians to tell others of the redeeming love of Christ and the eternal life they can have through him." And, with so many people on the verge of death, "AIDS has created an evangelism opportunity for the body of Christ unlike any in history."

The evangelical approach is now threatening Uganda's astonishing success in reining in HIV transmission. From the mid 1980s and the late 1990s, the number infected fell from an average of 17% of the population (and 30% in some urban areas) to little more than 6%. Academics, examining the phenomenon, pointed to the swift appreciation of Museveni of the challenge the country faced, the open and frank nature with which the epidemic was discussed and the extensive public education programme that was conducted in a non-judgmental tone in a wide range of mediums.

But perhaps most important to the sense of urgency was the extent of the pandemic. HIV and Aids was affecting the whole country. Everyone knew someone, often in their own family, who was living with HIV or who had died from Aids. There was no room for doubt that something had to be done.

By the end of the 1990s, Uganda was being held up as a shining example of what could be achieved. At about the same time, the evangelical wing of the Christian churches started to make rapid inroads among the faithful and the lapsed of Uganda's towns and villages. By some accounts, as many as half of Uganda's Christians are now "born again".

Of all the messages about halting the spread of HIV and Aids, one particularly appealed to the evangelicals. "As simple as ABC", declared the billboards, and Abstain, Be faithful and Condom use - simple and memorable - came to be singled out as the key to Uganda's unequalled success. A message that changing personal behaviour in line with the church's teaching brought salvation in this world was elevated and refined until, for young people, it became encapsulated in a single imprecation: Abstain.

The person most identified with the message in Uganda is the president's wife, Janet. In 2003 she took the "True Love Waits" message to Washington in support of Bush's bid to Congress for $15bn of Aids funding. Although the great bulk of the funding was for the provision of antiretrovirals, $1bn was to support programmes promoting the message of abstinence - a message Bush was also encouraging to combat teen pregnancy in US schools.

"Religious organisations played a major role in prevention [of HIV/Aids] and had a strong influence," Janet Museveni told a Baptist conference in Washington DC. "When we adopted the True Love Waits slogan, we found that the most important thing was focusing on our spiritual foundation and values."

At the international Aids conference in Bangkok in 2004 the message was repeated by the Ugandan president, despite widespread criticism of the apparent downgrading of the importance of condom use, particularly in a country like Uganda that is in effect polygamous, and where women might abstain or be faithful, but with no confidence that their husbands will have done either.

By 2006, the evangelical focus on abstinence was being challenged by other Christian churches, which recognised that the inequality of women made negotiating either abstinence or safe sex impractical.

Supported by the African Network of Religious Leaders Living with Aids, a wider approach was devised, which included the core message of abstinence and fidelity, but in a non-hierarchical context. HIV is a disease, they argued, not a moral issue.

SAVE (acronyms seem indispensable) stands for Safer sex, Available medication, Voluntary counselling and testing, and Empowerment and negotiation. In 2006, to strong criticism from the evangelicals, it was adopted by the charity Christian Aid.

Beatrice Ware, a prominent Ugandan HIV campaigner, who has been infected with HIV by her husband, says: "ABC stigmatises HIV positive women. It allows people to conclude that we are either promiscuous or unfaithful."

Winnie Sseruma, a Ugandan who works for Christian Aid, says it also leaves children born with HIV in despair. "How did I get it, they ask? They wonder what they did wrong."

But evangelicals, like those in Anglican Mainstream group, accuse Christian Aid of succumbing to political correctness. Not for the first time, the Christian churches find themselves torn between a compassionate approach and a strictly moral one.

Sseruma believes it is not only the abstinence message promoted by evangelical Christians that is behind the halt in the fall of HIV transmission in Uganda. "The evangelical churches distort the message around healing," she says. "People take it to mean that prayer alone can heal, but it should be made clear that God can't do it alone. People must keep taking their medication."

Most intractable is the fate of homosexual Africans, condemned by society in general and evangelicals in particular, unable to seek treatment and often compelled by peer pressure into marriage, ensuring the cycle of transmission is renewed.

Sseruma fears that, encouraged by the evangelical churches, society is becoming less and less tolerant of those living with HIV. Individuals convicted of infecting someone can now be imprisoned. Soldiers are denied promotion. The open, non-judgmental approach to HIV education and treatment that saw such success in the 1990s is being progressively undermined in a politico-religious movement that is financially endorsed by Bush's Republicans.