To clarify the role of coffee in health, we assessed the role of coffee consumption in T2DM, IHD, CVD risk factors (lipids, glycemic traits, adiposity and adiponectin), depression and Alzheimer’s disease using genetic determinants of coffee from genome-wide association studies (GWAS) applied to very large extensively genotyped case-control and cross-sectional studies. This evidence concerns the gene ADIPOQ and type 2 diabetes mellitus.