Matrix metalloproteinases (MMPs) play a pivotal role in remodeling the extracellular matrix (ECM) and are therefore of interest for new diagnostic tools for the clinical management of diseases involving ECM disruption. This setting ranges from the classical areas of MMP studies, such as vascular disease, cancer progression or bone disorders, to new emerging fields of application, such as neurodegenerative disease or sepsis. Increasing the knowledge about the role of MMPs in the pathogenesis of diseases where a clear diagnostic panel is still lacking could provide new insight and improve the identification and the clinical treatment of these human diseases. This review focuses on the latest descriptions of the clinical use of MMP as biomarkers in the diagnosis, prognosis and monitoring of different diseases, such as diabetes, cardiovascular diseases, cancer and metastasis, neurodegenerative disorders and sepsis.