OBJECTIVE: To compare the extent of intestinal schistosomiasis among school children attending school in an irrigation and non-irrigation area of Central Kenya. DESIGN: A cross sectional study. SETTING: Three separate parasitological surveys involving four primary schools in Mwea irrigation scheme, Kirinyaga District and two from a non-irrigation area in Machakos District. SUBJECTS: One thousand two hundred and twenty two children aged between five and nineteen years were examined for Schistostoma mansoni infection by Kato thick smear technique. RESULTS: High prevelances ranging from 73% to 94% were noted among children in all the participating schools. Overall 41% of the infected children had heavy infection (>400 eggs per gram), 27% had moderate infection (101-400 epg) and 32% had light infection (10-100epg). When data from the two areas were analysed seperately, peak eggs output were found in 5-9 year olds among children in Kirinyaga while this situation shifted to the 10-14 year olds in Machakos children. In Kirinyaga District, boys in the 10-14 years age group had a significantly higher output than girls (P<0.01), but this situation was reversed in the older children (P<0.05). Girls in Machakos District had consistently but non-significantly higher output than boys. CONCLUSION: Intestinal schistomiasis is more prevalent and with a higher intensity in the irrigated than in non-irrigated areas. There were also pronounced age and gender related differences in the pattern of infection between the two study areas.