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Background: Schistosomiasis is one of the most important neglected tropical diseases, with a great impact on public health and more than 200,000 deaths annually. Schistosoma haematobium causes urinary tract (UT) morbidity. Since schistosomiasis morbidity control programs focus on children older than 5 years, pre-school age children (PSAC) morbidity is not well known. Methods: We conducted a cross-sectional study in Cubal (Angola) among 245 PSAC with the objective of evaluating the prevalence of S. haematobium infection, the intensity of infection, and associated morbidity. For this purpose, urine filtration test followed by microscopic visualization and ultrasound examinations were performed. Results: The estimated overall prevalence of urogenital schistosomiasis was 30.2% (CI 95%; 24.5–35.9), with 20.3% (CI 95%; 15.3–25.3) of the samples analysed showing a high intensity of infection. A total of 54.5% (CI 95%; 47.6–61.8) of infected children presented UT lesions, showing a significant association between schistosomiasis infection and UT morbidity (p-value < 0.001). Bladder wall thickening was the most common lesion, being present in 100% of abnormal ultrasounds. We found that anaemia and severe malnutrition were not significantly associated with the development of UT lesions. Conclusions: S. haematobium infection in PSAC causes great UT detectable morbidities. Therefore, there is an evident need of including them in mass drug administration (MDA) campaigns and consequently the development of an adapted praziquantel treatment dosage for children under 2 years of age. Author summary: Urogenital schistosomiasis caused by Schistosoma haematobium is a major public health problem in the impoverished population of tropical regions. The guidelines of the World Health Organization determine periodic mass drug administration with praziquantel as the main strategy to prevent morbidity associated with the chronic phase of the disease. This strategy has focused in school-age children, but recent recommendations suggest including other target populations, such as pre-school age children. In this study we evaluated the prevalence and morbidity associated with urogenital schistosomiasis in Cubal, an endemic area of Angola. We found a prevalence of urogenital schistosomiasis of 30.2% (CI 95%; 24.5–35.9) with a high infection intensity of 20.3% (CI 95%; 15.3–25.3) among pre-school age children. In addition, among the children infected, 54.5% (CI 95%; 47.6–61.8) presented urogenital abnormalities on ultrasound examination. There is an evident need of including them in mass drug administration campaigns and consequently the development of an adapted praziquantel treatment dosage for children under 2 years of age. [ABSTRACT FROM AUTHOR]