The article is devoted to the history of the formation and development of science in Karakalpakstan. It is stated that in 1931 the Karakalpak Integrated Research Institute was established in Turtkul. In the pre-war period, this institute was reorganized several times, as a result of which difficulties arose in coordinating scientific and research work in Karakalpakstan. In 1947, it was transferred to the Academy of Sciences of Uzbekistan. In 1959, the Karakalpak affiliate of the Academy of Sciences of the Uzbek Soviet Socialist Republic was organized on the basis of the Karakalpak Integrated Research Institute, which made it possible to coordinate and develop fundamental scientific research in the republic. The scientists focused on topical issues of the development of the economy and culture of the republic, in particular, the study of natural resources, material and spiritual culture of the Karakalpak people. The author claims that a new stage in the development of this scientific center begins in 1991, when the Karakalpak affiliate of the Academy of Sciences of the Republic of Uzbekistan receives the status of the Karakalpak branch. The author critically assesses the period of development of science in Karakalpakstan in the 1990s, while claiming that this scientific institution has risen to new stages of its development and certain achievements have been achieved.