The Pew Research Center's Forum on Religion and Public Life examined both government restrictions on religions and social hostility toward minority religious groups.
Egypt, especially, saw a great increase in religious intolerance in 2011, the report said.
"Before the Arab Spring, government restrictions on religion and social hostilities involving religion were higher in the Middle East and North Africa than in any other region of the world. Government restrictions in the region remained high in 2011, while social hostilities markedly increased," Pew said.
Harassment of Muslims increased in many countries, the report said.
Generally, the report found increases in religious restrictions around the world. For example, government restrictions on religion were up in Asia, while social hostility increased in sub-Saharan Africa.
There was movement in the opposite direction in a few places. Britain is taking steps to end the 18th-century ban on monarchs having Roman Catholic spouses, while Austria has loosened government restrictions on religion, the report found.