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Breast cancer is the most prevalent form of cancer in women worldwide and Iraq every year. Many clinical, diagnostic and pathological techniques have been in front to get early detection of breast tumors. The objective of this study was to assess urine neopterin and total neopterin levels in patients with stages II and III breast cancer. This study is a cross sectional study that was conducted between July 2019 to October 2019 in Medical City Hospital in Baghdad, Iraq. A total of 50 patients newly diagnosed with breast cancer were divided into two groups according to the obtained results in which; 30 patients newly diagnosed and untreated with stage II breast cancer, and 20 patients newly diagnosed and untreated with stage III breast cancer. Levels of neopterin and total neopterin were measured in all participants by High Performance Liquid Chromatography (HPLC) technique. The markers (neopterin, 7, 8-dihydroxy neopterin and total neopterin) in urine of breast cancer patients showed no significant correlations between the two stages breast cancer patients. A no significant correlation was found for neopterin between stages II and III in the urine of breast cancer patients in this study (P- value=0.482and, r=0.30).Total neopterin on the other hand showed no significant correlation between stages II and III in urine (P- value=0.962, and r= 0.2). The current study concluded the possibility of the potential clinical use of neopterin and total neopterin as useful markers in urine of breast cancer patients for diagnosing the different stages of the disease.