A number of minority groups within Islam have faced persecution by other Muslims for allegedly being incompatible with the regional majority of Islam. Accusation of heresy or apostasy can result in takfir (excommunication).

Ahmadis

The Ahmadiyya regard themselves as Muslims, but are seen by many other Muslims as non-Muslims and "heretics" since they are accused of not believing in the finality of prophethood since the death of Muhammad. Armed groups, led by the umbrella organization Khatme Nabuwwat ("Finality of Prophethood"), have launched violent attacks against their mosques in Bangladesh.

They committed massacres against them which resulted in 2,000 Ahmadiyya deaths in Pakistani Punjab. Eventually, martial law had to be established and Governor general Ghulam Mohamed dismissed the federal cabinet. This anti-Ahmadiyya movement led Pakistani prime minister Zulfiqar Ali Bhutto to declare that the Ahmadiyyas were "non-Muslims".Jamaat-i-Islami Federal Research Division US Library of CongressPersecution of the Ahmadiyya Community in Pakistan: An Analysis Under International Law and International Relations

In 1984, the Government of Pakistan, under General Zia-ul-Haq, passed Ordinance XX,Ordinance XX which banned proselytizing by Ahmadis and also banned Ahmadis from referring to themselves as Muslims. According to this ordinance, any Ahmadi who refers to oneself as a Muslim by words, either spoken or written, or by visible representation, directly or indirectly, or makes the call for prayer as other Muslims do, is punishable by imprisonment of up to 3 years. Because of these difficulties, Mirza Tahir Ahmad migrated to London, UK.

Ajlafs and Arzals

Despite the claims of Islam's egalitarian tenets, units of social stratification, termed as "castes" by many, have developed among Muslims in some parts of South Asia."Islamic caste." Encyclopædia Britannica. 2006. Encyclopædia Britannica Online. 18 Oct. 2006Burton-Page, J., Hindū, Encyclopaedia of Islam. Edited by: P. Bearman, Th. Bianquis, C. E. Bosworth, E. van Donzel and W. P. Heinrichs. Brill, 2006. Brill Online. Various theories have been put forward regarding the development of castes among Indian Muslims. Majority of sources state that the castes among Muslims developed as the result of close contact with Hindu culture and Hindu converts to Islam,Muslim Caste in Uttar Pradesh (A Study of Culture Contact), Ghaus Ansari, Lucknow, 1960, Page 66 while few others feel that these developed based on claims of descent from Muhammad.Sajida Sultana Alvi, Advice on the art of governance, an Indo-Islamic Mirror for Princes P122, State University of New York Press, Ahmad, Imtiaz, "The Ashraf-Ajlaf dichotomy in Muslim social structure in India", Indian economic and social history review 33 (1966) pgs 268-78

Sections of the ulema (scholars of Islamic jurisprudence) have declared the religious legitimacy of the caste system with the help of the concept of kafa'a. A classic example of scholarly literature supporting the Muslim caste system is the Fatawa-i Jahandari, written by the 14th century Turkish scholar, Ziauddin Barani, a member of the court of Muhammad bin Tughlaq, of the Tughlaq dynasty of the Delhi Sultanate. Barani was known for his intensely casteist views, and he regarded the Ashraf Muslims as racially superior to the Ajlaf Muslims.

He divided the Muslims into grades and sub-grades. In his scheme, all high positions and privileges were to be a monopoly of the high born Turks, not the Indian Muslims. Even in his interpretation of the Koranic verse "Indeed, the pious amongst you are most honored by Allah", he considered piety to be associated with noble birth. Barrani was specific in his recommendation that the "sons of Mohamed" [i.e. Ashrafs] "be given a higher social status than the low-born [i.e. Ajlaf]. His most significant contribution in the fatwa was his analysis of the castes with respect to Islam. His assertion was that castes would be mandated through state laws or "Zawabi" which would carry precedence over Sharia law whenever they were in conflict.

In the Fatwa-i-Jahandari (advice XXI), he wrote about the "qualities of the high-born" as being "virtuous" and the "low-born" as being the "custodians of vices". Every act which is "contaminated with meanness and based on ignominy, comes elegantly [from the Ajlaf]". Barani had a clear disdain for the Ajlaf and strongly recommended that they be denied education, lest they usurp the Ashraf masters. He sought appropriate religious sanction to that effect. Barrani also developed an elaborate system of promotion and demotion of Imperial officers ("Wazirs") that was conducted primarily on the basis of caste.

In addition to the Ashraf/Ajlaf divide, there is also the Arzal caste among Muslims, whose members were regarded by anti-Caste activists like Babasaheb Ambedkar as the equivalent of untouchables.Web resource for Pakistan or the Partition of India The term "Arzal" stands for "degraded" and the Arzal castes are further subdivided into Bhanar, Halalkhor, Hijra, Kasbi, Lalbegi, Maugta, Mehtar etc. The Arzal group was recorded in the 1901 census in India and its members are also called Dalit Muslims "with whom no other Muhammadan would associate, and who are forbidden to enter the mosque or to use the public burial ground". They are relegated to "menial" professions such as scavenging and carrying night soil.Dereserve these myths by Tanweer Fazal,Indian express

Alawites

The Alawites are a sub group of the Muslim faith that believes in the divine nature of Ali, the cousin of Muhammad.

Ibn Taymiyyah asserted that Alawites were not Shi'ites and were heretics outside Islam, arguably being the most virulent anti-Alawite in his fatwas where he stated that Alawites "are more infidel than Jews or Christians, even more infidel than many polytheists. They have done greater harm to the community of Muhammad than have the warring infidels such as the Franks, the Turks, and others. To ignorant Muslims they pretend to be Shi’is, though in reality they do not believe in God or His prophet or His book[...] Whenever possible, they spill the blood of Muslims[...] They are always the worst enemies of the Muslims[...] war and punishment in accordance with Islamic law against them are among the greatest of pious deeds and the most important obligations".The Nusayris are more infidel than Jews or Christians, even more infidel than many polytheists. They have done greater harm to the community of Muhammad than have the warring infidels such as the Franks, the Turks, and others. To ignorant Muslims they pretend to be Shi’is, though in reality they do not believe in God or His prophet or His book…Whenever possible, they spill the blood of Muslims…They are always the worst enemies of the Muslims…war and punishment in accordance with Islamic law against them are among the greatest of pious deeds and the most important obligations". – Ibn Taymiyyah, as quoted by Daniel Pipes (1992). Greater Syria. Oxford University Press. p. 163. . The Ottomans often relied on Ibn Taymiyya's religious rulings to justify their persecution of Alawites.

Alevis

Mutazilites

In medieval Iraq, the Mu'tazili theological movement was made a state doctrine in 832, igniting the Mihna (ordeal) a struggle over the application of Greek logical proof of the Qu'ran; people who would not accept Mu'tazili claims that the Qur'an was created rather than eternal were sometimes persecuted. The most famous victims of the Mihna were Ahmad Ibn Hanbal who was imprisoned and tortured, and the judge Ahmad Ibn Nasr al-Khuza'i who was crucified.“Do not envy anyone who has not been harmed for the sake of this affair.” « A Resource of Translated Islamic Texts Ahmad Ibn Hanbal was dragged before the inquisition, known as the Mihna, ordered by the caliph al-Maʾmūn.Ahmad ibn Hanbal – Britannica Online Encyclopedia

However, it lost official support soon afterwards. This coincided with the rise to prominence of the Ash'ari approach to Islam, of which Al-Ghazali was a staunch defender. Sunni and Shi'a Islam became the mainstream schools of Islam. As a consequence, the tables turned and some Mutazili scholars were victims of persecution themselves in the centuries to follow. Some Islamic philosophers like Averroes and Avicenna also faced persecution from fellow Muslims in their time.Science, civilization and society Mu'tazilite doctrine – by now regarded as heretical by Sunnis – continued to be influential amongst some Shia in Persia and Zaydis in Yemen.Ash'ariyya and Mu'tazila

Shi'a

Throughout history, Shi'as have faced genocide in Sunni majority locations. In 1513, Ottoman Sultan Selim I ("The Grim") ordered the massacre of 40,000 Shia "heretics" in Anatolia during the Safavid-Ottoman struggles.St Thomas More Studies The Ottoman Conquest

The Mughal emperor Aurengzeb is also recorded to have persecuted Shi‘a communities. His persecution of the Ismaili successor to Imam al-Din, or Imamshah, changed the course of the history of his community of followers. Common folk took up arms against the military and captured the fortress of Broach. However, their initial success did not last and, along with other sister communities, they were put down.

While some strand in Sunni regards Shiism as a valid madhhab, following Al Azhar, some Sunnis both now and in the past have regarded it as beyond the pale, and have attacked its adherents. In modern times, notable examples include the bombing campaigns by the Sunni Sipah-e-Sahaba against Shia mosques in Pakistan,RELIGION-PAKISTAN: Shia-Sunni Tensions Surface on Campus the genocide of Hazara under the Taliban,BBC News | SOUTH ASIA | Hazara people's long suffering and the bloody attacks linked with Zarqawi and his Sunni followers against Shia in Iraq.BBC NEWS | Middle East | Crushing Iraq's human mosaic

Some of the worst Shia-Sunni sectarian strife has occurred before (under Saddam regime responsible for at least 400,000 Shia deaths) and after the American invasion of Iraq.Civil War According to one estimate, as of early 2008, 1,121 Sunni suicide bombers have blown themselves up in Shia-majority Iraq.March 14, 2008 The Independent/UK "The Cult of the Suicide Bomber" by Robert Fisk "month-long investigation by The Independent, culling four Arabic-language newspapers, official Iraqi statistics, two Beirut news agencies and Western reports" Sunni suicide bombers have targeted not only thousands of civilians,over half of the 20,000 fatalities worldwide from terrorism in 2006 occurred in Iraq according to the American National Counterterrorism Center Report on Terrorist Incidents 2006 p.3 but mosques, shrines,Al Jazeera English – News – Car Bomb Blast Near Iraq Shrine wedding and funeral processions,Iraqi funeral procession bombed; at least 26 killed markets, hospitals, offices, and streets.

The Saudi Arabian government has been viewed as repressive against Shias living in Saudi Arabia, mainly because it encourages the Salafi faith, which denounces Shia Islam as heretical. Shias are mainly persecuted due to the belief that they are Iranian "puppets" and traitors. In several Saudi Arabian cities, Shia azans and Ashura demonstrations are banned.

Sunni

The Safavid conversion of Iran to Shia Islam was a process that took place roughly over the 16th through 18th centuries and turned Iran (Persia), which previously had a Sunni majority, into the spiritual bastion of Twelver Shi'ism. It was a process that involved forced conversion.

Ismail I consolidated his rule over the country and launched a thorough and, at times, brutal campaign to convert the majority Sunni population to Twelver Shiism and thus transform the religious landscape of Iran. The modern Middle East: a political history since the First World War. Mehran Kamrava, p. 29. His methods of converting Iran included: