In August 2012, a crowd of Sunni Muslims (Islam's largest denomination) attacked a community of minority Shiite Muslims in the Sampang regency on the island of Madura, part of East Java. They burned down dozens of houses belonging to Shiite members and killed two people. Views of what caused the violence differed greatly. Government officials declared the attacks to be rooted in a “family conflict” human rights activists held that the attack was carefully planned in advance and that a deep-seated mistrust towards members of the Sy'ia community concerning their religious beliefs was at the root of the Sy'ia–Sunni violence. They asserted that the violence was triggered by a group that had intended to stop a number of Shiite students from returning to their boarding school in the town of Bangil, East Java, after spending the holidays marking the end of the fasting month of Ramadan at home. After the Shiite students had reported the threats to the local police, around 1,000 attackers burned down their village.

The assault evoked memories of a similar incident in late 2011, when the home and pesantren (local boarding school) of a Madurese Shiite leader by the name of Tajul Muluk were destroyed. Tajul had been facing accusations of preaching that Islam's holy book, the Qur'an, was not God's original scripture and that its true and final version would only be revealed to the Mahdi, the prophesied redeemer of Islam at the end of times. In response to the charges, the local branch of the Indonesian Ulama Council (Majelis Ulama Indonesia [MUI]) released a fatwa (legal ruling) declaring Tajul's teachings to be “deviant”. The local district court subsequently charged Tajil with “defamation of religion”, which carries a maximum sentence of five years in prison.

These two incidents took place against a backdrop of increasing religious segregation and intolerance in Indonesia. Various surveys suggest that an increasing number of people harbour feelings of resentment and suspicion towards people of different religious convictions, in particular if these happen to live in the same neighbourhood. The most recent survey (at the time of writing), publicized in October 2012, put that share at 67.8 per cent.