RATIONALE Glycosylation of proteins and lipids is reliant on the availability of monosaccharide-activated donors known as sugar nucleotides. They are responsible for glycosylation in cells. Reliable quantification of these sugar nucleotides might provide an insight into their biological roles and attributes. METHODS Herein, a method is described for the quantification of sugar nucleotides using ultra high pressure liquid chromatography (UHPLC) tandem mass spectrometry, allowing selective detection of sugar nucleotides in a biological sample. Seven model sugar nucleotide standards commonly associated with lipid and protein glycosylation were separated on a porous graphitic carbon column using an UHPLC system coupled to a triple stage quadrupole mass spectrometer utilizing a multiple reaction monitoring approach. RESULTS Successful baseline separation of these metabolites was attained in 6 min using an ammonium formate buffer and acetonitrile, circumventing the use of MS-unfriendly pairing reagents. The linear dynamic range of this procedure was established over almost three orders of magnitude from 20 pg to 1 ng (40 pg to 2 ng for the isomers UDP-GlcNAc/GalNAc). The limit of detection ranged from 15 pg to 30 pg while the limit of quantification ranged from 50 pg to 100 pg. Furthermore, viability of this method was tested using three different breast cancer cell lines (MDA-MB-231, MDA-MB-231-BR, and MDA-MB-361) with the successful identification and quantification of all seven targeted sugar nucleotides. CONCLUSIONS The described method permitted the quantitative analysis of sugar nucleotides in 10 min, thus allowing the practical use of this approach in high-throughput settings. The method was also very effective for the quantification of sugar nucleotides derived from three different breast cancer cell lines. The distribution of sugar nucleotides was different among the different cell lines and unique for each cell line.