Christian legal group ADF International intervened in the case in support of the man known as A.A. (anonymised for security reasons) saying the asylum seeker could face severe social and formal persecution if sent home.
The Strasbourg Court Judges held that the Muslim who became a Christian would have been compelled to conceal their faith or face persecution if deported by the Swiss authorities.
Conversion from Islam to another religion is illegal in the Middle Eastern country and punishable by "anything from lengthy imprisonment to death", the human rights firm said.
Robert Clarke, Director of European Advocacy for ADF International insisted: "Nobody should be persecuted because of their faith. Our society has a responsibility to protect those who are facing torture, imprisonment, or death due to their religious beliefs. Afghanistan counts as one of the most dangerous countries in the world for Christians and, in particular, for converts.
"ADF International's intervention sought to highlight the severe breaches of human rights in Afghanistan against religious minorities and especially the widespread persecution of Christians. We welcome this important judgement from the European Court of Human Rights, affirming that Christians should not have to hide their faith to avoid persecution."
While the Afghan Constitution protects religious freedom in general, it also defines Islam as the state religion and prohibits the enactment of any law contradicting Islamic beliefs which creates a parallel legal system, ADF explained.
The systems' civil courts investigate "crimes against God". Blasphemy, anti-Islamic writings or speech, and conversion to other religions are considered serious and punishable by beheading for males, life imprisonment for females, confiscation of property, and inheritance limitations.
"Today, the Judges of the Strasbourg Court held that the applicant (identified only as 'A.A.') would be compelled to conceal their Christian faith and would in effect 'be forced to live a lie' if deported to Afghanistan by the Swiss authorities," said Lorcán Price, Legal Counsel for ADF International in Strasbourg.
"The Court was critical of the Swiss authorities and their failure to properly conduct an assessment of the risks and consequences of deporting a Christian convert to Afghanistan. It concluded that this was in breach of Switzerland's obligations to protect individuals from torture under the European Convention of Human Rights."
"We are glad that the Strasbourg Court has used this case to uphold the rights of Christians to openly profess their faith without facing the threat of physical violence, imprisonment, and possibly the death penalty. Switzerland, and every other member state of the European Convention on Human Rights, has an obligation in international law to protect those fleeing religious persecution," Price added.
Afghanistan is number two on Open Doors' World Watch List which ranks 50 countries where Christians face the most extreme persecution.
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