Detection of early drug abuse has driven the use of mass spectrometry in clinical laboratories across North America. Mass spectrometry-based assays have been increasingly implemented in various clinical disciplines for their advantages in high analytical sensitivity, specificity and multiplexing capacity. Mass spectrometry is now routinely used for the clinical analysis of small molecule compounds, peptides, proteins, clinical toxicology and microbiology. Although more FDA-approved platforms and reagents need to be commercially available, there is no doubt that mass spectrometry technology has demonstrated rich clinical applications.