BackgroundThe national burden of genito-urinary schistosomiasis in Nigeria has been expressed by an estimate of 101.3 million people at risk with an alarming figure of 29 million infected. Report obtained from respondents about Praziquantel® distribution and the obviously prevalent haematuria without any control programme in place justified the need for data on the prevalence, intensity of infection and associated risk factors which were the objectives this cross-sectional survey sought to address.MethodsA total of 718 students aged 10–23 years from the study area were surveyed between May and August, 2015. Data on socio-demographic and risk factors were obtained using structured questionnaires. Clean universal bottles with corresponding labels were offered for sample collection between 10:00 am and 13:30 pm. Centrifuged samples were microscopically examined and intensity of infection was recorded per 10 ml of each sample.ResultsPrevalence of genito-urinary schistosomiasis was 22.7 % with a mean intensity of 25.05 (± standard deviation, ± 71.51) eggs/10 ml of urine. Higher prevalence (19.5 %) and mean intensity (28.7 eggs/10 ml of urine) was recorded among boys. Sex (χ2 = 77.065, P < 0.0001), age group 16–18 (χ2 = 5.396, P = 0.0202), altitude (χ2 = 8.083, P = 0.0045), unwholesome water sources (χ2 = 27.148, P < 0.0001), human recreational activities (χ2 = 122.437, P < 0.0001), mothers’ occupation (χ2 = 6.359, P = 0.0117), farming (χ2 = 6.201, P = 0.0128) and other brown collar jobs (χ2 = 4.842, P = 0.0278) in fathers’ occupational category were found to be significantly associated with urogenital schistosomiasis. Boys were seven times more likely to be infected compared to girls [AOR (95 % CI): 7.3 (4.26–12.4)]. Age group 16–18 years was four times more likely to be infected compared to age group 10–12 years [AOR (95 % CI): 4.43 (2.62–7.49)]. Similarly, respondents with farming as fathers’ occupation were twice more likely to be infected than those whose fathers were civil servants [AOR (95 % CI): 2.08 (1.2–3.59)].ConclusionsDutsin-Ma and Safana were classified as moderate-risk Local Government Areas (LGA). Sex, altitude, unwholesome water sources and mothers’ occupation were identified as the determining epidemiological factors in the prevalence of the disease. Sustainable chemotherapeutic intervention with Praziquantel®, good network of treated pipe-borne water, health education and waste disposal facilities are highly recommended to reduce its prevalence below the threshold of public health significance.