There is a need for field-applicable markers to assess morbidity associated with intestinal schistosomiasis, especially in the context of preventive chemotherapy in young children. We investigated whether fecal occult blood (FOB) point-of-care tests could be used to assess intestinal pathology over a 12-month period in a cohort of 382 children (< 5 years of age). We found a strong association between egg-patent schistosomiasis and FOB at baseline (odds ratio [OR] = 3.1, P < 0.0001), 6 months (OR = 3.4, P < 0.0001), and 12 months (OR = 3.5, P < 0.0001), despite repeated chemotherapy. There were tendencies for prevalence of FOB to decrease in children who became egg negative and increase in those who became egg positive. Our results demonstrate overt disease in children less than five years of age. We therefore propose that FOB is useful for assessing dynamics of intestinal morbidity in young children at the community level and monitoring changes in morbidity after mass chemotherapy.