Chronic diseases, also known as noncommunicable diseases (NCDs), are complex disorders that last for long periods of time and progress slowly. They currently account for the major cause of death worldwide with an alarming increase in rate both in developed and developing countries. In this chapter, the principal metabolomic-based investigations on chronic diseases (cardiovascular diseases, diabetes, and respiratory chronic diseases) and their major risk factors (particularly overweight/obesity) are described by focusing both on metabolites and metabolic pathways. Additional information on the contribution of metabolomics strategies in the ambit of the biomarker discovery for NCDs is also provided by exploring the major prospective studies of the last years (i.e., Framingham Heart Study, EPIC, MONICA, KORA, FINRIK, ECLIPSE). The metabolic signature of diseases, which arises from the metabolomic-based investigation, is therefore depicted in the chapter by pointing out the potential of metabolomics to explain the pathophysiological mechanisms underlying a disease, as well as to propose new therapeutic targets for alternative treatments.