In 2011, Kyrgyzstan reported no autochthonous cases of malaria. In 2013, the country officially applied to WHO for certification of malaria elimination in the country and the process was initiated in 2014. The country is expected to complete the certification process by the end of 2016.

Malaria was eradicated in Kyrgyzstan in 1959, but a few local cases were registered annually beginning in 1986, as a result of the imported cases in military personnel returning from Afghanistan. The years 1986 and 1987 saw 14 and 10 autochthonous malaria cases reported, respectively. In 1988, 21 cases due to local transmission were registered, 11 of which occurred in the Batken district, bordering Tajikistan and Uzbekistan. Up until 1995, only imported cases were reported in the country.

In 1996, the first case of autochthonous malaria was registered in the Panfilov district. Afterwards, the number of autochthonous malaria cases rose, despite a reduction in imported malaria.

In 2002, the explosive resumption of malaria transmission produced an epidemic. A total of 2267 autochthonous Plasmodium vivax cases were reported in the south-western regions of the country, including Batken, Osh and Jalal-Abad. The resumption of malaria transmission in Kyrgyzstan resulted from the immigration of a number of infected people from Tajikistan into the Batken region, where the Anopheles vector exists and conditions for malaria transmission are very favourable.

In 2004 the first autochthonous case of P. falciparum malaria was reported in the Aravan district of the southern part of Kyrgyzstan, in an area bordering Uzbekistan. In 2005, the number of autochthonous cases of P. vivax malaria increased in the outskirts of Bishkek.

As a result of the application of epidemic control measures, the reported number of autochthonous malaria cases decreased significantly during 2004–2010 and no cases were reported in 2011.

The highest malariogenic potential is found in the southern regions of the country, including the Osh, Batken and Jalal-Abad areas, primarily due to the many rice plantations there. Malaria vectors in these areas include An. pulcherimus, An. superpictus, An. hyrcanus, An. martinius, An. claviger and An. messeae. Studies on vector resistance to different insecticides have proven all the above-mentioned species susceptible to DDT, fenitrothion, cyfluthrin, deltamethrin, malathion, lamba-cyhalothrine and propoxur.