IntroductionMalaria has been the leading cause of morbidity and mortality for several decades in Mali, with an increase from 2017 to 2020 (2,884,837 confirmed cases and 1,454 deaths). On the recommendation of the World Health Organization (WHO) and in the interests of efficient use of resources, Mali has begun a process of stratifying the health districts to target malaria control strategies.MethodMalaria, entomological and environmental data were collected through the local health information system (LHIS), the Demographic and Health Survey (DHS 2018), research institutions and MALI-METEO services. The WHO has recommended stratification at the district level consisted of assigning each district to one of 4 classes according to criteria based on incidence adjusted for attendance rate. Variables associated with monthly malaria incidence at the district level were identified using a general additive non-linear regression model.ResultsFrom 2017 to 2019, the median incidence across 75 health districts of Mali was 129.34 cases per 1,000 person-year (IQR=86.48). The results showed different periods of high malaria transmission in health districts level and durations varying from 2 to 6 months, showing a double peak for some health districts, which were located in the flooded areas. environmental variables such as rainfall, vegetation index (NDVI), maximum temperature and relative humidity were significantly associated at malaria incidence with a lag of around one month. A strata defines a geographical area with similar epidemiological, environmental and socio-economic factors. Stratification resulted in 12 health districts of very low transmission, 19 low transmission, 20 moderate transmission and 24 in high transmission areas. The number of rounds of season malaria chemoprevention will be based on the number of months in the high transmission period.ConclusionThis first stratification in Mali will allow targeting malaria control strategies. This approach will be dynamic and revised yearly in order to integrate information from the national epidemiological surveillance.