Certain gases in the breath are known to be indicators of the presence of diseases and clinical conditions. These gases have been identified as biomarkers using equipments such as gas chromatography (GC) and electronic nose (e-nose). GC is very accurate but is expensive, time consuming, and non-portable. E-nose has the advantages of low-cost and easy operation, but is not particular for analyzing breath odor and hence has a limited application in diseases diagnosis. This article proposes a novel system that is special for breath analysis. We selected chemical sensors that are sensitive to the biomarkers and compositions in human breath, developed the system, and introduced the odor signal preprocessing and classification method. To evaluate the system performance, we captured breath samples from healthy persons and patients known to be afflicted with diabetes, renal disease, and airway inflammation repectively and conducted experiments on medical treatment evaluation and disease identification. The results show that the system is not only able to distinguish between breath samples from subjects suffering from various diseases or conditions (diabetes, renal disease, and airway inflammation) and breath samples from healthy subjects, but in the case of renal failure is also helpful in evaluating the efficacy of hemodialysis (treatment for renal failure).