We developed a complete method to measure low [ 13 C] enrichments in glycogen. Fourteen rats were fed a control diet. Six of them also ingested either [U- 13 C] glucose (n=2) or a mixture of 20 [U- 13 C] amino acids (n=4). Hepatic glycogen was extracted, digested to glucose and purified on anion–cation exchange resins. After the optimization of methylboronic acid derivatization using GC–MS, [ 13 C] enrichment of extracted glucose was measured by GC–C-IRMS. The accuracy was addressed by measuring the enrichment excess of a calibration curve, which observed values were in good agreement with the expected values (R=0.9979). Corrected delta values were −15.6±1.6 δ 13 C (‰) for control rats (n=8) and increased to −5 to 8 δ 13 C (‰) ‰ and 12–14 δ 13 C (‰) ‰ after the ingestion of [U- 13 C] amino acids or [U- 13 C] glucose as oral tracers, respectively. The method enabled the determination of dietary substrate transfer into glycogen. The sequestration of dietary glucose in liver glycogen 4h after the meal was 35% of the ingested dose whereas the transfer of carbon skeletons from amino acids was only 0.25 to 1%.