Chlorogenic acid (CGA), an important biologically active dietary polyphenol, is produced by certain plant species and is a major component of coffee. Reduction in the risk of a variety of diseases following CGA consumption has been mentioned in recent basic and clinical research studies. This systematic review discusses in vivo animal and human studies of the physiological and biochemical effects of chlorogenic acids (CGAs) on biomarkers of chronic disease. We searched PubMed, Embase, Amed and Scopus using the following search terms: ("chlorogenic acid" OR "green coffee bean extract") AND (human OR animal) (last performed on April 1st, 2015) for relevant literature on the in vivo effects of CGAs in animal and human models, including clinical trials on cardiovascular, metabolic, cancerogenic, neurological and other functions. After exclusion of editorials and letters, uncontrolled observations, duplicate and not relevant publications the remaining 94 studies have been reviewed. The biological properties of CGA in addition to its antioxidant and anti-inflammatory effects have recently been reported. It is postulated that CGA is able to exert pivotal roles on glucose and lipid metabolism regulation and on the related disorders, e.g. diabetes, cardiovascular disease (CVD), obesity, cancer, and hepatic steatosis. The wide range of potential health benefits of CGA, including its anti-diabetic, anti-carcinogenic, anti-inflammatory and anti-obesity impacts, may provide a non-pharmacological and non-invasive approach for treatment or prevention of some chronic diseases. In this study, the effects of CGAs on different aspects of health by reviewing the related literatures have been discussed.