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Religious persecution is systematic mistreatment of an individual or group due to their religious affiliation.
In a secular state, claims of religious persecution are effectively a demand of the fulfilment of Freedom of religion and Religious pluralism. In a non-secular state, they are laments about the intolerance of the state religion and the demand for Religious toleration or disestablishment.
Often it is the alleged persecution of individuals within a group in the attempt to maintain their religion identity, or the exercise of power by an individual or organization that causes members of a religious group to suffer. Persecution in this case may refer to unwarranted arrest, false imprisonment, beatings, torture, unjustified execution, denial of benefits, and denial of civil rights and liberties and especially other acts of violence, such as war, torture, and ethnic cleansing.It also may refer to the confiscation or destruction of property, or incitement to hate among other things.
Not only theorists of secularization (who presume a decline of religiosity in general) would willingly assume that religious persecution is a thing of the past. However, with the rise of fundamentalism and religiously related terrorism this assumption has become even more controversial. Indeed, in many countries of the world today, religious persecution is a human rights problem.

Reasons for religious persecution

Main article: Religious intolerance Persecution for heresy and blasphemy
More than 300 Roman Catholics were put to death by English governments between 1535 and 1681 for treason, thus for secular than religious offences. This dramatically worsened the situation of the Catholics in England. English governments continued to fear Popish Plot;

Persecution for political reasons
Out of Egypt came monotheistic Judaism under Moses, its prophet. Among the Ten Commandments of the new religion was one that forbade the worship of any other god than its one true God. When Imperial Rome extended its reach to their area, various conflicts arose.
Out of Judaism came Christianity, which because it was strictly monotheistic and also encouraged conversion was a much more powerful threat to the established pantheistic order than had been Judaism. The Jewish exemption from the requirement to participate in public cults was lifted and the anti-monotheistic religious persecution of the Christians began under Nero.
By the eighth century Christianity had attained a clear ascendancy in Europe and neighboring regions and a period of consolidation began marked by the pursuit of heretics and various other forms of monotheistic religious persecution. Christian monotheistic religious persecution perhaps reached its apex with the Inquisition.
Meanwhile south and east of the Christian empires yet another monotheist religion had arisen: Islam. Generally following the Jewish tradition of tolerance towards non-believers provided they maintained the outward habits of believers, Muslims spread across northern Africa, the Middle East, northern India, and adjoining regions. Those who actively oppose Islam or try to persuade people in their community not to convert to Islam may face persecution or death threats (which may even be carried out). At times, attempts at peaceful persuasion against Islam have led to persecution.
See also: Historical persecution by Christians, Persecution of Ancient Greek religion

Historical persecution
Since the 18th century there have been many occasions where religious persecution has occurred.

Present Period

Main article: Persecution of Bahá'ís Bahá'ís in Iran

Main article: anti-Semitism Judaism
It is estimated that over 1.5 million Christians have been killed by the Janjaweed, the Arab Muslim militia, and even suspected Islamists in northern Sudan since 1984.

Christianity
Some people believe that both the United States and Al-Qaeda are involved in religious persecution. The September 11, 2001 attacks on the United States have been suspected by religious figures of happening because of America's relative secularity; though, it should be noted that Al Qaida never once in their public statements used that as a justification for 9/11 or any other attack. The reasons Al Qaida give for their attacks are the presence of American troops in Saudi Arabia, the location of Islam's holy sites, which they consider sacrilege, the occupation of Muslim territory, and American financial support of Israel.
Christian churches have been bombed in Pakistan and there have been attempted attacks on churches elsewhere. Tunisia, Saudi Arabia, Istanbul in Turkey etc have been attacked, mainly because these governments are seen by the extremists to be collaborating with foreign non-Islamic powers.
On the other hand, shortly after September 11 there was a sharp increase of Islamophobia in the United States and the United Kingdom, where Muslims are sometimes attacked in public or even killed [5]. The 21st century "War on terror" was at one point referred to as a "crusade" until the Muslim understanding of the term was pointed out, and abuses by American soldiers during the invasion of Iraq in 2003 (e.g. the Abu Ghraib prisoner abuse) made some Muslims felt that they were being persecuted, therefore giving rise to anti-American feelings, coordinated attacks by extremist Islamic groups and insurgency in the Middle East.

United States and Islam

Main article: anti-Mormon United States and Mormonism
The government of People's Republic of China in mainland China has banned the spiritual group Falun Gong and conducted massive crackdown of the group, including using torture and "re-education" camp to force the adherents to abandon Falun Gong. There are reports indicating that the PRC has engaged in organ harvesting from live Falun Gong adherents, among other human rights abuses.

People's Republic of China
Religious persecution and discrimination have been an official part of U.S. governmental policies and law regarding Native Americans. For example, traditional indigenous ceremonies such as the Sun Dance and Ghost Dance were officially outlawed in the late 1800s.
In modern times, charges of religious persecution by the U.S. government against Native Americans continue. These charges have largely centered on the eagle feather law which governs the possession of eagle feathers for religious use, the use of ceremonial peyote, and the repatriation of Native American human remains and cultrual and religious objects found in museums and private collections.
The eagle feather law, which governs the possession and religious use of eagle feathers, was officially written to protect then dwindling eagle populations while still protecting traditional Native American spiritual and religious customs, of which the use of eagles are central. The eagle feather law later met charges of promoting racial and religious discrimination due to the law's provision authorizing the possession of eagle feathers to members of only one ethnic group, Native Americans, and forbidding Native Americans from including non-Native Americans in indigenous customs involving eagle feathers — a common modern practice dating back to the early 1500s.
Peyote, a spineless cactus found in the desert southwest and Mexico, is a commonly used in certain traditions of Native American religion and spirituality, most notably in the Native American Church. Prior to the passage of the American Indian Religious Freedom Act (AIRFA) in 1978, and as amended in 1994, the religious use of peyote was not afforded legal protection. This resulted in the arrest of many Native Americans and non-Native Americans participating in traditional indigenous religion and spirituality. Many individuals today encounter harassment and persecution by their employers for ingesting peyote while participating in the Native American Church due to the cactus containing the psychotropic mescaline, a controlled substance.
Native Americans often hold strong personal and spiritual connections to their ancestors and often believe that their remains should rest undisturbed. This has often placed Native Americans at odds with archaeologists who have often dug on Native American burial grounds and other sites considered sacred, often removing artifacts and human remains – an act considered sacrilegious by many Native Americans. For years, Native American communities decried the removal of ancestral human remains and cultural and religious objects, charging such activities as acts of genocide, religious persecution, and discrimination. Many Native Americans called on the government, museums, and private collectors for the return of remains and sensitive objects for reburial. The Native American Graves Protection and Repatriation Act (NAGPRA), which gained passage in 1990, established a means for Native Americans to request the return or "repatriation" of human remains and other sensitive cultural, religious, and funery items held by federal agencies and federally assisted museums and institutions.

United States and Native Americans

"I have come from a country where people are hanged if they talk." — Leonhard Euler
"Religious persecution has come about because others are too afraid to learn about something new..." — Zachary Jensen
"No orthodox church ever had power that it did not endeavor to make people think its way by force and flame. And yet every church that ever was established commenced in the minority, and while it was in the minority advocated free speech -- every one. John Calvin, the founder of the Presbyterian Church, while he lived in France, wrote a book on religious toleration in order to show that all men had an equal right to think; and yet that man afterward, clothed in a little authority, forgot all his sentiments about religious liberty, and had poor Serviettes burned at the stake, for differing with him on a question that neither of them knew anything about. In the minority, Calvin advocated toleration -- in the majority, he practiced murder." — Robert Green Ingersoll. Literature