While supercritical fluid chromatography was developed over 50 years ago, it is only over the past 15 to 20 years that it has become routinely utilized. Along with the commercialization of a new generation of instruments, during the last 20 years supercritical fluid chromatography has improved performance, reliability, and robustness. Supercritical fluid chromatography is fully compatible with mass spectrometric techniques. This review compiles the application of supercritical fluid chromatography separations coupled to mass spectrometry instrumentation for the exploration, profiling, and quantitation of metabolites during the last two decades. The selection of metabolites chosen for this article have direct applications in preclinical models of disease and clinical applications as potential biomarkers of disease including lipids, steroid hormones, bile acids, polar metabolites, peptides, and proteins.