Metabolic profiling with stable-isotope tracers in combination with gas chromatography/mass spectrometry (GC/MS) is a well-established technique for measuring substrate redistribution within metabolic pathways. This analysis relies on the ability to localize and quantify the fractional incorporation of 13C isotope into each carbon atom of precursor-derived metabolites. In this paper, several carbohydrate derivatization procedures (peracetylation, deuterioalditol acetates, and aldononitrile acetates) are evaluated for the positional isotopic information obtained by gas chromatography/electron impact mass spectrometry (GC/EI-MS). These derivatives have been compared for the quantitative evaluation of 13C distribution into isotopomers of 13C-labeled aldoses and ketoses, and the fragmentation pathways for 15 hexoses, pentoses, and amino sugars of biological origin have been assessed. In addition, a new type of carbohydrate derivative (dialkyldithioacetal acetates) has been developed for GC/MS that retains the charge on the anomeric carbon of the original monosaccharide. Electron impact ionization of these derivatives generates well-resolved base peaks arising from C1-C2 bond cleavage with charge retention at the C1 thiol groups. The dialkyldithioacetal acetates are uniquely well suited for measuring isotopic enrichment into the characteristic anomeric carbon of aldose sugars and will facilitate the global analysis of metabolic flux in carbohydrate pathways.