Mass spectrometry has a strong history in drug-metabolite analysis and has recently emerged as the foremost technology in endogenous metabolite research. The advantages of mass spectrometry include a wide dynamic range, the ability to observe a diverse number of molecular species, and reproducible quantitative analysis. These attributes are important in addressing the issue of metabolite profiling, as the dynamic range easily exceeds nine orders of magnitude in biofluids, and the diversity of species ranges from simple amino acids to lipids to complex carbohydrates. The goals of the application of mass spectrometry range from basic biochemistry to clinical biomarker discovery with challenges in generating a comprehensive profile, data analysis, and structurally characterizing physiologically important metabolites. The precedent for this work has already been set in neonatal screening, as blood samples from millions of neonates are tested routinely by mass spectrometry as a diagnostic tool for inborn errors of metabolism. In this review, we will discuss the background from which contemporary metabolite research emerged, the techniques involved in this exciting area, and the current and future applications of this field.