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Abstract Background The control of schistosomiasis in Nigeria is mainly by mass treatment with praziquantel through the school system, with an absence of any provision for pre-school children. We therefore determined the prevalence and intensity of urinary schistosomiasis in pre-school children between the ages of 1-6 years in Ilewo-Orile a rural and endemic community, near Abeokuta, Nigeria as part of providing information on the neglected tropical diseases among this age group. Two urine samples were collected from each pre-school child. The samples were tested for microhaematuria using reagent strips and then processed and examined with a microscope for Schistosoma haematobium ova. Results Of the 167 children examined 97 (58.1%) had infection, with no significant difference (P = 0.809) in infection rates between boys (57.1%) and girls (59.2%). Both prevalence and intensity of infection did not increase significantly with age (P = 0.732). The overall geometric mean egg count was 1.17 eggs/10 ml urine. There was no significant association (P = 0.387) between intensity in boys (1.16 eggs/10 ml urine) and girls (1.19 eggs/10 ml urine). 47.4% of the children had microhaematuria which did not increase significantly with age (P = 0.526). Focus group discussions with guardians and caregivers revealed that infection of pre-school children early in life was due to exposures through bathing in the stream by their mothers, while the older children would visit the stream for washing, fetching of water, bathing and swimming. Conclusion Community participatory health education is needed in this community as a first step in reducing infection and transmission of the disease, while the rehabilitation and repair of the existing water borehole system in the community should be effected. The results of this study have shown that pre-school children also harbour infection and are a source of transmission of schistosomiasis in endemic communities. Planning and provision for their treatment should be considered in control programmes.