Since its discovery and over the approximately 500 years of studying coffee’s effects, its relationship with health, both nutritionally and medically, has been extensively researched, with positive views regarding its use predominating. Coffee has long been recommended as a panacea for a wide range of diseases, such as infectious diseases, as well as chronic diseases such as cardiovascular disease or cancer. The role of coffee in health and disease has been influenced by the theoretical and methodological scientific trends of the time, starting with medieval medicine and ending with genetic medicine. Despite the controversies regarding its use and abuse, which over time led to the approval or restriction of coffee consumption, its connection to health and disease has evolved as new information emerged about its nutritional, medical and pharmacological potential.