Primitive religion and Shamanism were practiced by the ancestors of the Uygurs before Zoroastrianism, Buddhism, Manichaeism, Nestorianism and Islam were introduced into the region. During the period spanning the Tang and Song dynasties, Buddhism was the predominant religion practiced by the nobility and the common people in the Uighur Kingdom of Gaochang and the Kingdom of Khotan. Many Uighurs converted to Nestorianism during the Yuan Dynasty. Today in Xinjiang, a significant number of people do not follow any religion, and many Uygurs follow religions other than Islam.

The introduction of Islam into Xinjiang was related to the emergence of the Arab Empire and the eastward expansion of Islam. The Uighur conversion to Islam was not a voluntary choice made by the common people, but a result of religious wars and imposition by the ruling class, though this fact does not undermine our respect for the Muslims' right to their beliefs. Islam is neither an indigenous nor the sole belief system of the Uygur people.

In the process of accepting Islam, the ancestors of the Uygurs and Kazaks integrated it with local faiths and traditions, while absorbing the cultures of other ethnic groups in the region and from inland areas. Some of their religious concepts, rituals and customs remained as they evolved. Through interaction with these elements, Islam in Xinjiang gradually developed distinct local and ethnic features. For example, orthodox Islam does not allow the worship of anyone or anything other than Allah. However, the Uygurs and some other ethnic groups still venerate mazars, which are mausoleums or shrines, typically of saints or notable religious leaders. Mazar worship is a prominent example of the localization of Islam in Xinjiang. The practice of erecting long poles around the mazars, hung with streamers and sheepskin, is a result of influence from multiple religions including Shamanism and Buddhism. As another example, the Baytulla Mosque in Yining and the Shaanxi Mosque in Urumqi, both first built in Emperor Qianlong's reign (1736-1795) during the Qing Dynasty, are characterized by beam-column construction which was common in inland areas. This embodies a form of localization of Islam.

It should be noted that since the late 1970s and early 1980s, and in particular since the end of the Cold War, the surge in religious extremism around the world has caused a rise in religious extremism in Xinjiang. This has resulted in an increasing number of incidents of terror and violence that pose a serious danger to social stability and to the lives and property of people in the region. Under the guise of religion, religious extremism trumpets theocracy, religious supremacism, actions against "pagans", and "holy wars". It instigates terror and violence and incites hostility between different ethnic groups, running counter to the teachings concerning patriotism, peace, solidarity, the golden mean, tolerance, and good works advocated by Islam and many other religions. Religious extremism, which constitutes the ideological base of ethnic separatism and terrorism, is by nature anti-human, anti-society, anti-civilization, and anti-religion. It is a betrayal of religion and should never be confused with religious matters, or be glossed over or excused through religious rhetoric. Drawing lessons from international experiences and in view of reality of the region, Xinjiang has taken resolute action to fight terrorism and extremism in accordance with the law, effectively clamp down on terrorism and violence and the spread of religious terrorism. Through these efforts Xinjiang has responded to the public's expectation of security for all ethnic groups, protected the basic human rights, and maintained social harmony and stability in the region. Xinjiang's fight against terrorism and extremism is a battle for justice and civilization against evil and barbaric forces. As such it deserves support, respect and understanding. Some countries, organizations and individuals that apply double standards to terrorism and human rights have issued unjustified criticism of Xinjiang's effort. This kind of criticism betrays the basic conscience and justice of humanity, and will be repudiated by all genuine champions of justice and progress.