Abstract Background Urogenital schistosomiasis caused by Schistosoma heamatobium is one of the major public health problems worldwide. It is thought that despite extensive efforts and integrated control programs implicated over the last few decades, the global disease burden of schistosomiasis remains unacceptably high. This persistence of the disease may be due to in part the lack of accurate diagnostic tools for case detection and community screening in endemic areas. Aim of the work The present work aims to develop a novel nano-diagnostic assay using gold nanoparticles (nanomagnetic beads based- ELISA) which can utilize larger surface area, achieving a higher sensitivity for detection of urinary schistosomal egg antigen (SEA) in urine of human schistosomiasis haematobium and comparing it with the traditional sandwich ELISA and direct microscopic examination of urine sediments together with indirect screening by chemical reagent strips for microhaematiria and proteinuria for assessing prevalence of urinary schistosomiasis in some villages in Beni-Suef governorate. Subjects and methods A cross sectional study was conducted on 290 students (192 male and 98 female) selected randomly from Primary and Preparatory schools in four villages in Beni-Suef governorate; The participating children were aged 8–15 years old. A simple questionnaire was designed based on the key indicators of urinary schistosomiasis then, terminal urine samples were collected between 10 am and 2 pm in clean container from each participant to be screened by chemical reagent strips (Combi 10) and examined by urine microscopy and sandwich ELISA techniques (traditional and IMB) for S. haematobium detection. Soluble egg antigen (SEA) was used to produce specific polyclonal antibodies (pAbs) which were then used as a primary capture in the sandwich ELISA techniques. The anti-SEA pAbs were labeled with horse-radish peroxidase (HRP) and used as a secondary capture. Results Out of the 290 participants, 39 children (13.4%) were positive by UM, 53 were positive by traditional sandwich ELISA, with diagnostic sensitivity (87.2%) and specificity (92.4%) and 50 were positive by IMB-sandwich ELISA with diagnostic sensitivity (94.9%) and specificity (95.2%)based on UM results. Micro-haematuria and proteinuria were assessed by chemical reagent strips which gave sensitivity of 29.5%, specificity of 90.8% for micro-haematuria alone, sensitivity of 18.4%, specificity of 92.4% for proteinuria alone, while sensitivity of 35.9%, specificity of 94.9% for combined micro-haematuria and proteinuria which indicated a highly significant association with S. haematobium infection (p value<0.001). Conclusion Combination of both clinical and epidemiological data in addition to sensitive diagnostic tools is essential for diagnosis. The present study as with other studies revealed that, IMB-ELISA based on gold nanoparticles provides more rapid and sensitive detection for SEA in urine samples of patient with active schistosomiasis. Simplicity and fast detection (10 min) are its main advantages. Moreover, its high sensitivity and specificity ensure its application with greater precision and rapid detection. Also, in addition, the prevalence of urinary schistosomiasis in these regions is considered relatively high requiring rapid implementation of control programs to decrease the prevalence and improve the community's health status.