The Middle Turkic languages are the direct ancestor of the Karluk languages, including Uyghur and the Uzbek language.
Kagan Arik wrote that Modern Uyghur is not descended from Old Uyghur, rather, it is a descendant of the Karluk language spoken by the Kara-Khanid Khanate. According to Gerard Clauson, Western Yugur is considered to be the true descendant of Old Uyghur, and is also called "Neo-Uyghur". Modern Uyghur is not a descendant of Old Uyghur, but is descended from the Xākānī language described by Mahmud al-Kashgari in Dīwānu l-Luġat al-Turk. According to Frederik Coene, Modern Uyghur and Western Yugur belong to entirely different branches of the Turkic language family, respectively the southeastern Turkic languages and the northeastern Turkic languages. The Western Yugur language, although in geographic proximity, is more closely related to the Siberian Turkic languages in Siberia. Robert Dankoff wrote that the Turkic language spoken in Kashgar and used in Kara Khanid works was Karluk, not (Old) Uyghur.
Robert Barkley Shaw wrote, "In the Turkish of Káshghar and Yarkand (which some European linguists have called Uïghur, a name unknown to the inhabitants of those towns, who know their tongue simply as Túrki), ... This would seem in many case to be a misnomer as applied to the modem language of Kashghar". Sven Hedin wrote, "In these cases it would be particularly inappropriate to normalize to the East Turkish literary language, because by so doing one would obliterate traces of national elements which have no immediate connection with the Kaschgar Turks, but on the contrary are possibly derived from the ancient Uigurs".
Probably around 1077, a scholar of the Turkic languages, Mahmud al-Kashgari from Kashgar in modern-day Xinjiang, published a Turkic language dictionary and description of the geographic distribution of many Turkic languages, Dīwān ul-Lughat al-Turk (English: Compendium of the Turkic Dialects; Uyghur: تۈركى تىللار دىۋانى Türki Tillar Diwani). The book, described by scholars as an "extraordinary work," documents the rich literary tradition of Turkic languages; it contains folk tales (including descriptions of the functions of shamans) and didactic poetry (propounding "moral standards and good behaviour"), besides poems and poetry cycles on topics such as hunting and love, and numerous other language materials. Other Kara-Khanid writers wrote works in the Turki Karluk Khaqani language. Yusuf Khass Hajib wrote the Kutadgu Bilig. Ahmad bin Mahmud Yukenaki (Ahmed bin Mahmud Yükneki) (Ahmet ibn Mahmut Yükneki) (Yazan Edib Ahmed b. Mahmud Yükneki) (w:tr:Edip Ahmet Yükneki) wrote the
Hibat al-ḥaqāyiq (هبة الحقايق) (Hibet-ül hakayik) (Hibet ül-hakayık) (Hibbetü'l-Hakaik) (Atebetüʼl-hakayik) (w:tr:Atabetü'l-Hakayık).
Middle Turkic languages, through the influence of Perso-Arabic after the 13th century, developed into the Chagatai language, a literary language used all across Central Asia until the early 20th century. After Chaghatai fell into extinction, the standard versions of Uyghur and Uzbek were developed from dialects in the Chagatai-speaking region, showing abundant Chaghatai influence. Uyghur language today shows considerable Persian influence as a result from Chagatai, including numerous Persian loanwords.
Modern Uyghur religious literature includes the Taẕkirah, biographies of Islamic religious figures and saints. The Taẕkirah is a genre of literature written about Sufi Muslim saints in Altishahr. Written sometime in the period between 1700 and 1849, the Chagatai language (modern Uyghur) Taẕkirah of the Four Sacrificed Imams provides an account of the Muslim Karakhanid war against the Khotanese Buddhists, containing a story about Imams, from Mada'in city (possibly in modern-day Iraq) came 4 Imams who travelled to help the Islamic conquest of Khotan, Yarkand, and Kashgar by Yusuf Qadir Khan, the Qarakhanid leader. The shrines of Sufi Saints are revered in Altishahr as one of Islam's essential components and the tazkirah literature reinforced the sacredness of the shrines. Anyone who does not believe in the stories of the saints is guaranteed hellfire by the tazkirahs. It is written, "And those who doubt Their Holinesses the Imams will leave this world without faith, and on Judgement Day their faces will be black ..." in the Tazkirah of the Four Sacrificed Imams. Shaw translated extracts from the Tazkiratu'l-Bughra on the Muslim Turki war against the "infidel" Khotan. The Turki-language Tadhkirah i Khwajagan was written by M. Sadiq Kashghari. Historical works like the Tārīkh-i amniyya and Tārīkh-i ḥamīdi were written by Musa Sayrami.
The Qing dynasty commissioned dictionaries on the major languages of China which included Chagatai Turki language, such as the Pentaglot Dictionary.
Shaw and Christian missionaries such as George W. Hunter (missionary), Johannes Avetaranian, Magnus Bäcklund, Nils Fredrik Höijer, Father Hendricks, Josef Mässrur, Anna Mässrur, Albert Andersson (missionary), Gustaf Ahlbert, Stina Mårtensson, John Törnquist, Gösta Raquette,
Oskar Hermannson, the convert to Christianity Nur Luke, Harold Whitaker, and Turkologist Gunnar Jarring studied the Uyghur language and wrote works on it, calling it "Eastern Turki". Shaw wrote in his book that it was Europeans at his time who called the language "Uighur" while the native inhabitants of Yarkand and Kashgar did not call it by that name and but called it "Turki", and Shaw wrote that the name "Uighur" was a misnomer when referring to Kashgar's language. A Turkish convert to Christianity, Johannes Avetaranian went to China to spread Christianity to the Uyghurs. Yaqup Istipan, Wu'erkaixi, and Alimujiang Yimiti are other Uyghurs who converted to Christianity.
The Bible was translated into the Kashgari dialect of Turki (Uyghur).
The historical term "Uyghur" was appropriated for the language that had been known as Eastern Turki by government officials in the Soviet Union in 1922 and in Xinjiang in 1934. Sergey Malov was behind the idea of renaming Turki to Uyghurs. The use of the term Uyghur has led to anachronisms when describing the history of the people. In one of his books the term Uyghur was deliberately not used by James Millward. The name Khāqāniyya was given to the Qarluks who inhabited Kāshghar and Bālāsāghūn, the inhabitants were not Uighur, but their language has been retroactively labelled as Uighur by scholars. The Qarakhanids called their own language the "Turk" or "Kashgar" language, and did not use Uighur to describe their own language, Uighur was used to describe the language of non-Muslims but Chinese scholars have anachronistically called a Qarakhanid work written by Kashgari as "Uighur". The name "Altishahri-Jungharian Uyghur" was used by the Soviet educated Uyghur Qadir Haji in 1927.