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Abstract Background Rheumatic heart disease (RHD) is the most common acquired heart disease occurring in children and adolescents. RHD is associated with significant morbidity and mortality particularly in low and middle- income countries (LMICs) where the burden is estimated to be higher compared to high income countries. Subclinical RHD is the presence of valvular lesion diagnosed by echocardiography in a person with no clinical manifestation of RHD. This study aimed at determining the prevalence, types and factors associated with subclinical RHD among primary school children in Dar Es Salaam, Tanzania. Methods A descriptive community-based cross-sectional study was conducted in primary school children from February to May 2019. A standardized structured questionnaire was used to collect demographic characteristics, history of upper respiratory tract infections (URTIs), anthropometric measurements, and chest auscultation findings. Moreover echocardiographic screening was done to all children recruited into the study. World Heart Federation echocardiographic classification was used to define the types and prevalence of subclinical RHD. Results A total of 949 primary school children were enrolled with females being predominant (57.1%). The prevalence of subclinical RHD was 34 per 1000. All the participants had mitral valve disease only whereby 17 had definite disease and 15 had a borderline disease. The associated factors for subclinical RHD were older age of more than 9 years (OR 10.8, 95% CI 1.4–82.2, P = 0.02) having three or more episodes of URTI in previous six months (OR 21, 95% CI 9.6–46, P = 0.00) and poor hygiene (OR 3, 95% CI 1.3–6.8, P = 0.009). Conclusion Subclinical RHD as detected by echocardiographic screening is prevalent in primary school children, uniformly affects the mitral valve, and is associated with potentially modifiable risk factors. Children with a history of more than three episodes of URTI in six months represents a high-risk population that should be targeted for RHD screening.