The development and progression of many human diseases often result in changes in gene expression and protein and metabolite concentrations. Changes at the protein and metabolite level often are detectable in biological fluids and tissues before the appearance of clinical symptoms, rendering them useful diagnostic and prognostic biomarkers. As with many conditions, the discovery of a sensitive and specific urinary biomarker for bladder cancer would save lives and reduce the suffering due to this condition. A number of potential urinary protein biomarkers for bladder cancer have been identified, but they lack the sensitivity and specificity required to replace cystoscopy and histopathology. We discuss the use of mass spectrometry and nuclear magnetic resonance spectroscopy for the detection of metabolites in biological samples, comment on their advantages and limitations, and discuss recently published work in urine metabolic profiling for bladder cancer detection.