Urogenital schistosomiasis, due to Schistosoma haematobium, is one of the helminth infections of public health importance in sub-Saharan Africa where children carry the heaviest burden of infection. Treatment with the drug praziquantel is the only widely available tool for control. Current schistosome control programs are essentially school-based and exclude younger pre-school children. However, increasing reports of significant infection levels in this age group call for the inclusion of these young children in control programs. The hygiene hypothesis suggests that helminth infections, including schistosome infection, may protect against atopy, implying that helminth eradication may carry a detrimental burden of immune disorders. However, this conjecture is controversial. This study was designed to investigate the relationship between schistosome infection and atopy. In a comparative epidemiological approach between two schistosome endemic areas with differing infection levels, it is shown that atopy is inversely associated with current schistosome infection intensity but not with cumulative history of infection. This inverse relationship was subsequently shown to be associated with the levels of soluble CD23, the low affinity IgE receptor, but not with the polyclonal IgE stimulation. However, while praziquantel treatment was associated with an increase in schistosome-specific responses, a decline in atopic responses was observed in these communities, suggesting that treatment differentially affect anti-schistosome and atopic responses. In addition, the study has shown that praziquantel treatment of preschool age children increases, quantitatively and qualitatively, their schistosome-specific antibody responses purportedly associated with resistance to schistosome infection/reinfection.