We assessed morbidity indicators for both Schistosoma haematobium and Schistosoma mansoni infections and evaluated the appropriateness of the World Health Organization (WHO) guidelines for ultrasound in schistosomiasis in the context of large-scale control interventions. Abdominal and urinary tract ultrasonography was performed on 2,247 and 2,822 school children, respectively, from 29 randomly selected schools in Mali before the implementation of mass anthelminthic drug administration. Using two-level logistic regression models, we examined associations of potential factors with the risk of having a positive ultrasound global score (morbidity indicative of S. haematobium infection), abnormal image pattern scores, dilatation of the portal vein, and/or enlarged liver (morbidity indicative of S. mansoni infection). The WHO protocol was found useful for detection of S. haematobium pathology but overestimated the risk of portal vein dilatation and left liver lobe enlargement associated with S. mansoni infection. We conclude that ultrasonography should be included in large-scale control interventions, where logistics allow, but cautiously.