A High Performance Capillary Electrophoresis method for the detection and quantification of phosphorylated aldoses has been developed using D-thyminose (2-deoxy-D-ribose) as internal standard. The addition of an indolyl chromophor system to the carbonyl groups in the carbohydrates by reductive tryptamination resulted in high sensitivity by UV detection at 220 nm, and opportunities for identification based on the diode array spectrum with specific peaks at 220 and 280 nm. D-glucose 6-phosphate, D-ribose 5-phosphate, and the glycolytic intermediate DL-glyceraldehyde 3-phosphate were detected within 25 min, the analytes showing linearity in the concentration range from 2.5 to 100 mmol/L with correlation coefficients between 0.9290 and 0.9887. Detection and quantification limits were found to be from 210 to 450 μmol/L and from 360 to 750 μmol/L, respectively. The occurrence of two quantitatively dominating products from reductive tryptamination of D-ribose 5-phosphate and DL-glyceraldehyde 3-phosphate are believed to be a result of initial Maillard reactions. The two reaction products were separated and characterised using liquid chromatography and spectroscopy including NMR. The method proved to be an efficient tool to study the concentration of phosphorylated aldoses in pork revealing differences in concentration of the dominating aldose glucose-6-phosphate in different breeds of pig.