National Natural Science Foundation of China; Department of Science & Technology of Fujian Province [2009D023]; Medical Center Construction Foundation of Xiamen ; The clinical exploration of urinary metabonomic analysis on discriminating between the top-two-incidence urological cancers, bladder and kidney cancers (BC and KC), is still virgin land. In this study, we discovered and evaluated the clinical utility of holistic metabonomic profiling and current single biomarker methods, and ultimately suggested a potential screening test for BC and KC. Urine metabonomic profiling for 19 BC patients, 25 KC patients, and 24 healthy controls was carried out using an LC-MS based platform, which utilized both reversed phase chromatography and hydrophilic interaction chromatography. The holistic method that refers to orthogonal partial least-squares-discriminant analysis based on all qualified profile data, successfully classified BC, KC and healthy control groups, showing 100 % sensitivity and specificity. Taurine, hippuric acid, phenylacetylglutamine and carnitine species contributed most to the BC and KC discrimination. The predictive power of each above metabolite is evaluated using receiver operator characteristic technique. Hippuric acid was found 10-fold decrease in concentration relative healthy controls, and performed the best as a biomarker for BC diagnosis, with its sensitivity and specificity of 78.9 and 86.5 %, respectively. Carnitine C10:3 was found 1.5-fold decrease, and reached 84.0 % of sensitivity and 60.5 % of specificity for KC diagnosis. In view of both sensitivity and specificity, the holistic method is more accurate for detecting BC and KC, than current single metabonomic biomarker methods, and it could be advocated as a prescreen to other forms of more invasive or uncomfortable screening. Moreover, this approach also demonstrates attractive performance in diagnosis of early stage (ES) BC and KC patients.