Objective · To investigate the gender-related metabolomic differences in human saliva.  Methods · The saliva metabolomic profiles of 5 male and 5 female healthy volunteers with matched age, body mass index (BMI), living and tooth-brushing condition were acquired using ultra-high performance liquid chromatography with quadrupole time-of-flight mass spectrometry. Metabolites were identified using publicly accessible databases and further confirmed individually with standard compounds. Both multivariant and univariate statistics were conducted to find inter-gender differences.  Results · Forty-eight metabolites in human saliva were identified including 13 amino acids, 6 choline metabolites, 15 carnitines, 4 sphinganine metabolites, 7 lysophosphatidylcholine and 3 organic acids. Levels of phenylalanine, acetylcarnitine, propionylcarnitine, butyrylcarnitine, isobutyrylcarnitine, isovalerylcarnitine and sphinganine were higher in the saliva of females than that of males.  Conclusion · Rich metabolic information present in human saliva with significant gender diffference which ought to be taken into consideration in study on the metabonomics of saliva.