The persecution of religious minorities in Eritrea remains a major concern. In its annual International Religious Freedom report 2007, the US State Department said that the Eritrean government's record on religious freedom had deteriorated even further. There are reportedly 1,900 prisoners held for their religious beliefs in this small African nation.

The country's population of 3.7 million is roughly half Christian and half Muslim. Since 1995, the government only officially recognizes four faiths – the Eritrean Orthodox Church (the biggest church in Eritrea with an estimated 1.7 million adherents), Islam, the Lutheran Church and the Roman Catholic Church. In May 2002, the government insisted that all unregistered groups stop operating until they had obtained official approval. According to research undertaken by the UK-based Royal Institute of International Affairs (RIIA) at Chatham House, the Baha'i faith, the Faith Mission Church, the Orthodox Presbyterian Church and Seventh Day Adventists did manage to register, but have not been allowed to operate publicly.

However, many evangelical churches have not been registered. According to RIIA, these have reportedly been growing rapidly in Eritrea – although exact membership figures are hard to come by – and their followers have been particularly targeted by the government. In September 2007, the BBC interviewed an Eritrean evangelical Christian who described the torture techniques which had been used on him – including being tied in a position known as 'the Helicopter' for 136 hours. Another victim reported that he was held for 12 months, forced to do manual labour and, on one occasion, 'suspended by his arms from a tree in the form of a crucifixion'.

The 'Open Doors' Christian charity reported that at least four Christians had died in 2007, following severe ill-treatment at the hands of the authorities. Jehovah's Witnesses are treated with particular harshness because their faith prohibits them from undertaking Eritrea's compulsory military service, in some cases being held without trial for up to 12 years.

In a rare success, the prominent gospel singer Helen Berhane was released in November 2006, after an international campaign led by Amnesty International. She had been held for two and a half years – most of the time in a metal shipping container, which served as a cell. In late 2007 she was granted asylum in Denmark.

Even followers of the officially recognized religions have not been immune from harassment and ill-treatment. The deposed Patriarch of the Eritrean Orthodox Church, Abune Antonios, has been under house arrest for over two years.

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