Background: Neglected Tropical Diseases are a group of 13 major disabling conditions commonest among the world’s poorest people (Hotez, et al. 2007). Together, they contribute to a disease burden that is halfof all Malarias(Peter J. Hotez 2009). The diseases affect 2.7billion people that mainly live on less than $2 a day, are common in Sub-Saharan Africa, Latin America and Asia (Tchuente 2011). In the last fifteen years, Uganda’s Ministry of Health (MOH) has conducted Mass Drug Administration (MDA) in NTD infected communities with the support of various agencies such as WHO, USAID, ENVISION/RTI, SCI, DFID and Carter Center (RTI 2011). MDA against Schistosomiasis using PPraziquantel (PZQ) and mass education on prevention has been conducted in schools and communities. The prevalence of Schistosmiasis reduced between 2003 and 2007, however the prevalence has increased since 2007 due to unsafe hygienic environment (MOH-UG 2017). The Mayuge district has trained about 1,384 teachers and 1,536 Community Medicine Distributors to support the NTD program. However little success has been realized today. This has been attributed to several challenges including shortage of medicines, lack of behaviour change, failure to reach the most at-risk population, failure to adhere to drug compliance among others. Further still, there has been limited documentation of prevalence studies conducted in Mayuge to ascertain the impact of the program and inform better programming. World Vision in collaboration of Korea International Agency (KOICA), designed a three-year project to address Soil Transmitted Helminthe (STH) and Schistosomiasis using WHO recommending mass drug administration(MDA) integrated control through WASH, and health education and increase awareness. The project will conduct prevalence studies before project implementation to understand magnitude of the diseases and use results for targeted implementation. Given that assumption of environment factors affect to SCH prevalence, the project uses ecological modelling for the prevalence study. After the project, another prevalence study shall be conducted to assess its impact on the reduction of the disease prevalence and make recommendations to MoH. Methods: We used an ecological modelling approach to determine the prevalence of SCH depending on the risk of exposure to potential vectors since it varies depending on natural environments such as temperature (Brown 1994); (Moodley, et al. 2003), precipitation ((DeWitt 1995); (O’keeffe 1985), soil type(Ekpo, et al. 2008) level of vegetation cover (Brown 1994), (O’keeffe 1985) land-use change and water availability (Xing-jian, et al. 1999), suitable elevation (Kloos, et al. 1998)and slope (Zhu, et al. 2015) are the main factors that are associated with the prevalence of schistosomiasis where considered. The approach was preferred to provide important information on identifying risk populations to enable an increase in the efficiency of schistosomiasis disease control (Magalhães, et al. 2014). Results: A total of 1167 children were selected from thirty schools across Mayuge district. The final sample included 1123 children, 49% boys and 51% girls. 863 samples (76.8%) were from students and 260 (23.2%) were non-school children. Age was classified into 5 groups; 7-10, 11, 12, 13, and 14-17 years. The mean age of the sample was 11.9 ± 1.4 years. The district was divided into four infection risks categorized as Very low, low, high and very high according to climate and geographic information. Student hookworm infection was 15.5% (p=0.5074) while control (non-school) was 13.9% (P=0.1706). Prevenances for S. Mansoni were 28.2% and 23.9%, for Students and Control groups respectively (p = 0.1706), while STH was 15.8%. The results on regional risk category indicated a higher prevalence in low or very low-risk regions than in high or very high-risk regions. Prevalence’s of all parasites were higher among boys than girls. Hookworm prevalence was 4.9% higher, S. Mansoni 3.4%, and any STH 5.5%. The infection prevalence tended to increase with age. The intensity of infection among children with S.Mansoni was mainly light (12.7%). Moderate (7.3%) and heavy (7.2%) infections were almost the same. A similar pattern was observed for hookworm infection with 14.8% of 15.1% infections light. There were significant differences between infections for children that lived near the lake or river (44.7%) compared to those that didn’t (15.2%, P=<0.0001) for S. Mansoni and any infections. Awareness and knowledge of infection route, hand washing behaviour with soap and lack of proper drinking water sources were all associated with reduced infections. However, incoherence was observed among infections of children that had anthelmintic and shoe protection as they had higher hookworm infection compared those without. Conclusions: There is a continued need for preventive chemotherapy forSTH and S. mansoni across Mayuge district, despite not being high-risk to achieve elimination and also because the district is predominately high risk. Slight differences in hookworm, STH and S. Mansonipr evalence between children that do and do not report school attendance were observed during the study. This suggests the importance of not implementing targeted intervention but blanket for all children in the target age category if resources allow.