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Background  In 2012, the Kenyan Ministries of Health and of Education began a programme to deworm all school-age children living in areas at high risk of soil-transmitted helminths (STH) and schistosome infections. The impact of this school-based mass drug administration (MDA) programme in Kenya is monitored by the Kenya Medical Research Institute (KEMRI) as part of a five-year (2012–2017) study. This article focuses on the impact of MDA on STH infections and presents the overall achieved reductions from baseline to mid-term, as well as yearly patterns of reductions and subsequent re-infections per school community.    Methods  The study involved a series of pre- and post-intervention, repeat cross-sectional surveys in a representative, stratified, two-stage sample of schools across Kenya. The programme contained two tiers of monitoring; a national baseline and mid-term survey including 200 schools, and surveys conducted among 60 schools pre- and post-intervention. Stool samples were collected from randomly selected school children and tested for helminth infections using Kato-Katz technique. The prevalence and mean intensity of each helminth species were calculated at the school and county levels and 95 % confidence intervals (CIs) were obtained by binomial and negative binomial regression, respectively, taking into account clustering by schools.    Results  The overall prevalence of STH infection at baseline was 32.3 % (hookworms: 15.4 %;  Ascaris lumbricoides : 18.1 %; and  Trichuris trichiura : 6.7 %). After two rounds of MDA, the overall prevalence of STH had reduced to 16.4 % (hookworms: 2.3 %;  A. lumbricoides : 11.9 %; and  T. trichiura : 4.5 %). The relative reductions of moderate to heavy intensity of infections were 33.7 % (STH combined), 77.3 % (hookworms) and 33.9 % ( A. lumbricoides ). For  T. trichiura,  however, moderate to heavy intensity of infections increased non-significantly by 18.0 % from baseline to mid-term survey.    Conclusion  The school-based deworming programme has substantially reduced STH infections, but because of ongoing transmission additional strategies may be required to achieve a sustained interruption of transmission.    Electronic supplementary material  The online version of this article (doi:10.1186/s13071-016-1679-y) contains supplementary material, which is available to authorized users.

Monitoring the impact of a national school based deworming programme on soil-transmitted helminths in Kenya: the first three years, 2012 – 2014