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Background: Intestinal schistosomiasis is still a public health problem in Burundi. Since 2008, annual mass drug administration with praziquantel has been rolled out in 11 endemic districts. The national programme relies on school-based surveys with kato-katz to monitor the impact of mass drug administration. We explored whether routine data on intestinal schistosomiasis as determined by direct fecal smears at health centre level could be used., Methods: From the Burundian National Health Information System, we collected routine incidence data on intestinal schistosomiasis as determined by direct smear examination in all 45 sanitary districts during 2011-2015. A temporal trends analysis was performed using a mixed negative binomial regression. Sanitary districts with mass drug administration campaigns with praziquantel (n = 11) were compared with those without (n = 34). In addition, prevalence data on intestinal schistosomiasis based on kato-katz results from a school-based national mapping in 2014 were compared with the incidence data in health centres based on direct smear results, in the same 45 sanitary districts., Results: In the 11 sanitary districts applying mass drug administration with praziquantel, the incidence rate decreased significantly for the years 2014 (β 2014 = - 0.826, P = 0.010) and 2015 (β 2015 = - 1.294, P < 0.001) and for the five-year period (β = - 0.286, P < 0.001), whereas in the 34 districts where mass drug administration was not delivered, there was no significant decrease over time (β = - 0.087, P = 0.219). In most of the 45 sanitary districts, the low prevalence based on kato-katz in school children was confirmed by low incidence rates based on direct smears in the health centres., Conclusions: National Health Information System surveillance data, based on routinely collected direct smear results at health centre level, may be able to monitor the impact of mass drug administration with praziquantel on intestinal schistosomiasis in Burundi. Control and elimination of intestinal schistosomiasis call for integration of adequate diagnosis and treatment into routine activities of primary health care facilities, as recommended by the World Health Organization since more than 20 years. When moving towards elimination, more sensitive tests, such as the point-of-care circulating cathodic antigen assay are desirable.