Background: Biomarkers are good potential tools for early cancer diagnosis. Here we have analyzed eight different pteridines in the urine samples of cancer patients and compared them with samples from healthy subjects. Pteridines are important cofactors in the process of cell metabolism, and they have recently become a focal point of cancer screening research because certain pteridine levels have been shown to reflect the presence of cancers. Methods: We analyzed 8 pteridines; 6,7-dimethylpterin, 6-biopterin, d-(+)-neopterin, 6-hydroxymethylpterin, pterin, isoxanthopterin, xanthopterin and pterin-6-carboxylic acid using a house-built high-performance capillary electrophoresis with laser-induced fluorescence detection (HPCE-LIF). The levels of pteridines were reported as a ratio of pteridine to creatinine. Statistical hypothesis testing was conducted and P values were calculated to analyze the data. Results: Among the eight pteridines studied, 6-biopterin, 6-hydroxymethylpterin, pterin, xanthopterin, and isoxanthopterin levels were significantly higher in samples from cancer patients than in those from healthy subjects. Further, xanthopterin and isoxanthopterin levels were compared in breast cancer and lung cancer patients, but no significant difference was observed. Conclusion: Some pteridine levels can be used as biomarkers for noninvasive diagnosis of cancer; however, more data is needed to support this hypothesis.