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Background In 2016, diarrhea killed around 7 children aged under 5 years per 1000 live births in Burundi. The objective of this study was to estimate the economic burden associated with diarrhea in Burundi and to examine factors affecting the cost to provide economic evidence useful for the policymaking about clinical management of diarrhea. Methods The study was designed as a prospective cost-of-illness study using an incidence-based approach from the societal perspective. The study included patients aged under 5 years with acute non-bloody diarrhea who visited Buyenzi health center and Prince Regent Charles hospital from November to December 2019. Data were collected through interviews with patients’ caregivers and review of patients’ medical and financial records. Multiple linear regression was performed to identify factors affecting cost, and a cost model was used to generate predictions of various clinical and care management costs. All costs were converted into international dollars for the year 2019. Results One hundred thirty-eight patients with an average age of 14.45 months were included in this study. Twenty-one percent of the total patients included were admitted. The average total cost per episode of diarrhea was Int$109.01. Outpatient visit and hospitalization costs per episode of diarrhea were Int$59.87 and Int$292, respectively. The costs were significantly affected by the health facility type, patient type, health insurance scheme, complications with dehydration, and duration of the episode before consultation. Our model indicates that the prevention of one case of dehydration results in savings of Int$16.81, accounting for approximately 11 times of the primary treatment cost of one case of diarrhea in the community-based management program for diarrhea in Burundi. Conclusion Diarrhea is associated with a substantial economic burden to society. Evidence from this study provides useful information to support health interventions aimed at prevention of diarrhea and dehydration related to diarrhea in Burundi. Appropriate and timely care provided to patients with diarrhea in their communities and primary health centers can significantly reduce the economic burden of diarrhea. Implementing a health policy to provide inexpensive treatment to prevent dehydration can save significant amount of health expenditure.

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