To respond the growing demands for consuming natural foods, biochemical compounds originated from natural sources can be one of significant purposes for numerous researchers. In this review, we summarize the literatures regarding to the health effects of coffee consumption toward various human disease treatments, i.e., diabetes, cancer, liver diseases, and neurodegenerative diseases. The consumption of natural products is being common and considered significantly, for example, the potentially functional features of biochemical compounds contained in coffee have significantly contributed to clinical treatments of different human diseases. The experimental and epidemiologic evidences are indicated in this review to probably contribute to elucidate the protective effects of coffee consumption on several human diseases; besides, it is not still certain whether the consumption of coffee should be recommended to patients in some cases. Moreover, the chemical features and health benefits of coffee are introduced shortly, which can support readers understanding in detail to the benefits and the roles of coffee compounds.