Schistosomiasis control efforts mainly target school-aged children. We studied the epidemiology of schistosomiasis in two high-risk communities in south Côte d'Ivoire, placing particular emphasis on pre-school-aged children. We used a suite of diagnostic techniques, including Kato-Katz, urine filtration, reagent strips, and urine circulating cathodic antigen cassettes. Risk factors for schistosomiasis were determined by focus group discussions and a structured questionnaire. The prevalence of Schistosoma mansoni in the two study villages among the pre-school-aged children (age < 6 years) was 20.9% and 25.0%, whereas several-fold higher prevalences were found in school-aged children (58.7-68.4%) and adolescents/adults (59.5-61.7%). The prevalence of S. haematobium in the three age groups was 5.9-17.3%, 10.9-18.4%, and 3.8-21.3%, respectively. Most participants had light-intensity infections. Mothers' occupations and older siblings play important roles in the epidemiology of schistosomiasis in pre-schoolers. In the current epidemiologic settings, more attention is warranted on pre-school-aged children and adolescents/adults for successful schistosomiasis control.