Minorities' right to freedom of religion continued to give rise to concerns in 2007. The minority Baha'i, numbering approximately 2,000 at most, received a further setback in their attempts to be officially recognized when the Supreme Administrative Court reversed a lower court's decision earlier in the year to allow them to be officially registered for identity purposes. The result of this ruling was that Baha'is must continue to be registered as either Muslims, Jews or Christians. Refusal to do so entails the inability to obtain documentation ranging from birth certificates to other identification necessary to open bank accounts and send children to school. A government report in October 2006 argued that Baha'is must be 'identified, confronted and singled out so that they can be watched carefully, isolated and monitored in order to protect the rest of the population as well as Islam from their danger, influence and their teachings'.

Issues of religious freedom also arise in cases where individuals wish to convert to Christianity from Islam. Those who convert often do so quietly because of the harassment and intimidation from both the authorities, including the police, and religious groups. However, this approach was challenged in 2007, by the case of Mohammed Hegazy. According to reports, he undertook a court action to try to get his ID card changed to reflect his new Christian religion. His story was reported in national media, after which Mr Hegazy faced death threats and went into hiding. Mr Hegazy's case came amid a debate about apostasy, and its legitimate punishment. According to Associated Press reports, one of Egypt's most senior clerics, the Grand Mufti Ali Gomaa, issued guidance against the killing of apostates – a view which was rejected by other religious scholars in Egypt.

The minority Coptic Christians, estimated at 5–10 per cent of the overall population but concentrated more heavily in Cairo, Alexandria and the south, remained vulnerable through the year to attacks from Islamic extremists. In October 2007, two Copts were murdered at el-Kasheh, south of Cairo. Earlier in the year there were allegations of security force personnel destroying Coptic graves. There is currently internal debate among Copts over whether to support a possible presidential succession by Gamal Mubarak, regarded by some Copt leaders as their best guarantee of safety in the face of the Muslim Brotherhood.

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