To carry out a comparative cost-effectiveness analysis of screening methods for urinary schistosomiasis; terminal haematuria, unqualified haematuria, dysuria, visual urine examination and chemical reagent strip technique, in a school-based control programme. Estimation of costs and determination of cost-effect ratios of the screening methods applied in a school-based screening and treatment programme, from the perspective of a programme manager. A junior secondary school in Ibadan, Nigeria. Cost per number of cases correctly diagnosed. Unqualified haematuria was found to be the most cost-effective method costing N51.06 (US$ 2.16) to diagnose a case correctly, followed by terminal haematuria N58.91 (US$ 2.50) and dysuria N84.24 (US$ 3.57). Despite the relatively high input costs of chemical reagent strip technique over visual urine examination (N22.12 (US$ 0.94) per student vs. N6.44 (US$ 0.27) per student), it was found to be more cost effective costing N304.56 (US$ 12.91) to diagnose a case correctly than visual examination of urine cost of N317.58 (US$ 13.46) per correct case diagnosed. From the viewpoint of a programme manager, interview method of screening by asking for blood in the urine remains the most efficient means of screening for urinary schistosomiasis in school-based control programmes in our environment.