BackgroundTuberculosis is a serious global public health problem, and it is in the top 10 causes of mortality in low and middle income countries. MDR-TB and XDR-TB still being a challenge for clinicians and staff operating in national TB programs .Particularly in sub-Saharan African countries, it particularly coexists with high burden of other infectious and no communicable diseases, creating a complex public health situation which is difficult to address. Tackling this will require targeted public health intervention based on evidence well defines the at risk population. In this study, using data from two referral anti tuberculosis in Burundi, we model the determinants factors associated with MDR-TB in Burundi.MethodsProspective data of a sample of 180 tuberculosis randomly selected from a population of patients admitted in 2019 in two referral anti tuberculosis centres in Burundi: Kibumbu Sanatorium Centre and Bujumbura anti-tuberculosis Center. The associated factors were carried out by fixed and random effect logistic regression. Model performance was assessed by Area under Curve (AUC). Model was internally validated via bootstrapping with 1000 replications. All analysis were conducted in R 3.5.0.ResultsOver 180 participants of the study, 60 patients of them were MDR-TB and 120 were Drug Susceptible. High MDR-TB is observed in patients who lives in rural zone (51,3%),in collective residence (69,2%) ,in house with more than six people (59,5%), many people who live in the same room(70,0%) ,in patients with TB treatment history(86.4%) and in diabetics people(66.6%).HIV was 32.3% and 67.7% positive respectively in MDR-TB patients and Drug susceptible patients. More than half of cases (75%) and controls (73.3%) belonged to the age group of ≤ 45 years.The Pearson's Chi-squared test with Yates' continuity correction showed the house’s rooms (p = 0,010), People by house (p < 0,001), currently workers (p = 0,019), MDR-TB close contact (p < < 0.001), Collective residence (p = 0,004), Residence area (p = 0,007) and tobacco consumption (< 0.001) were not independent with MDR-TB.After modelling using fixed and random effects, Residence (AOR: 1.31, 95%CI: 1.12–1.80), People by house (AOR: 4.15, 95% CI: 3.06–5.39), MDR-TB close contact (AOR: 6.03, 95% CI: 4.01–8.12), History TB treatment (AOR: 2.16, 95% CI: 1.06–3.42), Tobacco consumption (AOR : 3.17 ,95% CI: 2.06–5.45) and Diabetes( AOR: 4.09,95% CI : 2.01–16.79) were statistically associated with MDR-TBs. With 2000 stratified bootstrap replicates, the model had an excellent predictive performance (AUC), accurately predicting 88.15%(95% CI: 82.06%-92.8%) of all observations. Drug susceptible patients with no close contact had the low probability around 10% to develop MDR-TB.ConclusionThe relatively high prevalence of tuberculosis and associated factors of MDR-TB in Burundi raises a call for concern especially in this context where there exist an equally high burden of chronic diseases, chronic malnutrition, HIV/SIDA and others infectious diseases. Targeting interventions based on these identified factors will allow judicious channel of resources and effective public health planning.