To control intestinal schistosomiasis at a national level in sub-Saharan Africa, there is a need for field-applicable markers to measure morbidity associated with this disease. The purpose of this study was to determine whether fecal calprotectin or fecal occult blood assays could be used as morbidity indicators for intestinal schistosomiasis. The study was carried out in Uganda with a cohort of young children (n = 1,327) and their mothers (n = 726). The prevalence of egg-patent schistosomiasis was 27.2% in children and 47.6% in mothers. No association was found between schistosomiasis infection and fecal calprotectin in children (n = 83, odds ratio [OR] = 1.08, P = 0.881), although an inverse relationship (n = 58, OR = 0.17, P = 0.043) was found in mothers. Fecal occult blood was strongly associated with Schistosoma mansoni infection in children (n = 814, OR = 2.30, P < 0.0001) and mothers (n = 448, OR = 1.95, P = 0.004). Fecal occult blood appears to be useful for measuring morbidity associated with intestinal schistosomiasis and could be used in assessing the impact of control programs upon disease.