Malaria was eradicated from Kazakhstan in 1967, and from 1968 only imported cases were reported. At the beginning of the 1990s, international contacts, including those with malaria-endemic countries, expanded considerably. In 1990–1997, the number of imported malaria cases registered in the country increased steadily, and the first case of locally transmitted malaria was reported in 1992. The number of such cases peaked at 7 in 2000.

During 1999–2001, 10 cases of autochthonous malaria were reported in southern Kazakhstan and Almaty. Since that time, there have been no reported cases.

On 20 March 2012, as a result of successfully maintaining the national territory of Kazakhstan free from malaria since 2001, WHO Director-General Margaret Chan has included the country in the list of countries that are officially acknowledged by WHO to be malaria-free.

The ecological and climatic conditions in most regions of the country could lead to a resurgence of malaria transmission following its importation. Parts of the Almaty, Jambyl and southern, western and eastern regions, as well as the cities of Almaty, Astana and Karaganda, pose the highest risk for a resurgence. Anopheles messeae, the most common malaria vector in Kazakhstan, is found throughout most of the county.