While research on alternative diagnostic and morbidity markers for infection with Schistosoma haematobium has been going on for a long time, egg counts continue to be used as the gold standard, and infection intensity is thought to reflect the severity of the disease. However, this relationship is not always clear and fluctuation in egg output makes it difficult to classify prevalence correctly. The use of circulating adult worm antigen detection as an alternative diagnostic technique has been applied with varying success. However, this is a measure of worm burden and does not reflect the tissue egg load(s). In the present study we have used an assay that detects soluble egg antigen (SEA) in urine of S. haematobium-infected children, and we have evaluated the applicability of the assay as a diagnostic and morbidity indicator. To evaluate this assay, we have studied a group of 470 children from two schools (Tsunguni and Kibaokiche) in the Coast province of Kenya; 84.8% and 77% were egg-positive while the percentage positive as determined by the SEA-ELISA were 78.8% and 76.2% in Tsunguni and Kibaokiche, respectively. In both schools, SEA levels in urine of S. haematobium-infected children significantly correlated with egg counts (Pearson's r=0.73, P < 0.0001) and with hematuria (Spearman's r=0.65, P < 0.0001). In addition, urinary tract pathology as determined by ultrasound significantly correlated with the SEA levels in urine (Spearman's r=0.3, P < 0.001). The SEA-ELISA compared well with microhematuria within egg count classes and with egg counts within hematuria classes.