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Growing up in a conservative Muslim household in rural West Sumatra, Alexander Aan hid a dark secret beginning at age 9: He did not believe in God. His feelings only hardened as he got older and he faked his way through daily prayers, Islamic holidays and the fasting month of Ramadan.

He stopped praying in 2008, when he was 26, and he finally told his parents and three younger siblings that he was an atheist — a rare revelation in a country like Indonesia, the world’s most populous Muslim-majority nation. They responded with disappointment and expressions of hope that he would return to Islam.

But Mr. Aan neither returned to Islam nor confined his secret to his family, and he ended up in prison after running afoul of a 2008 law restricting electronic communications. He had joined an atheist Facebook group started by Indonesians living in the Netherlands, and in 2011 he began posting commentaries outlining why he did not think God existed.

“When I saw, with my own eyes, poor people, people on television caught up in war, people who were hungry or ill, it made me uncomfortable,” Mr. Aan, now 32, said in an interview. “What is the meaning of this? As a Muslim, I had questioned God — what is the meaning of God?” He was released on parole on Jan. 27 after serving more than 19 months on a charge of inciting religious hatred.

Indonesia’s state ideology, Pancasila, enshrines monotheism, and blasphemy is illegal. However, the Constitution guarantees freedom of religion and speech, and the country is 16 years into a transition from authoritarianism to democracy.

But Mr. Aan’s case is one of an increasing number of instances of persecution connected to freedom of religion in Indonesia in recent years. Although Indonesia has influential Christian, Hindu and Buddhist minorities, every year there have been hundreds of episodes, including violent attacks, targeting religious minorities like Christians and Shiite and Ahmadiyah Muslims, as well as dozens of arrests over blasphemy against Islam. Numerous churches have been closed for lacking proper permits.

To be continued

He's lucky he wasn't killed

According to human rights organizations and various surveys, religious intolerance is on the rise in Indonesia, at least partly because of the growing influence of radical Islamic groups that use street protests and acts of violence to support their aims. Some of these radical groups demonstrated in Jakarta, the capital, before Mr. Aan’s trial in West Sumatra in 2012.

“His case very much ties in with that whole trend,” said Benedict Rogers, the East Asia team leader for Christian Solidarity Worldwide, a human rights organization founded in Britain. The group released a report in February warning that religious intolerance in Indonesia was spreading beyond traditionally conservative Muslim bases like West Java Province.

“Of course there would be religious people who would take offense about someone publicly expressing this view” about atheism, Mr. Rogers said. “But I think if it weren’t for this growing Islamism and extremism, Alexander’s case probably wouldn’t have happened.”

Mr. Aan’s troubles began in January 2012 when a mob in the Dharmasraya district of West Sumatra showed up looking for him at a government planning office where he worked as a data analyst.

“They wanted me to stop saying there is no God,” he said. “I told them that it was my right to express my beliefs.”

Police officers were called to prevent any violence, and they instead escorted Mr. Aan to the local police station, where he found himself being interrogated and, within hours, charged with disseminating information aimed at inciting religious hatred. The next day, he was charged with blasphemy and inciting others to embrace atheism.

A court in Padang, the capital of West Sumatra Province, threw out the blasphemy and atheism charges, but it convicted Mr. Aan in June 2012 of trying to incite religious hatred under the electronic information law and sentenced him to two and a half years in prison.