Fermentative catabolism of dietary and endogenous amino acids (AA) in the upper gut of pigs (FAAC) can result in significant loss of AA available for protein synthesis and body maintenance functions. A continuous infusion trial was performed using isotope tracers to determine ammonia flux in the upper gut, whole body urea flux, urea recycling (urea flux − urinary urea excretion), and FAAC (ammonia flux in the upper gut − urea recycling) in ileal-cannulated growing pigs fed a control diet (C, 19.3% CP), the control diet with added fibre (F, 12% pectin added at expense of cornstarch), or a diet low in protein (LP, 13.6% CP). 15N-ammonium chloride and 13C-urea were infused intragastrically and intravenously, respectively, for a period of 4 days. In samples obtained on days 3 and 4 of infusion, 15N-enrichments in blood urea (6.21 ± 1.65, 8.93 ± 2.01, and 9.78 ± 1.40 atoms percent excess (APE) for C, F and LP, respectively) were higher than those in ileal ammonia (0.44 ± 0.12, 0.37 ± 0.14, and 0.71 ± 0.10 APE). This suggests a rapid absorption of ammonia prior to the distal ileum and lack of uniformity for enrichment in the digesta ammonia pool. Simple isotope dilution calculations are, therefore, inadequate for calculating FAAC and ammonia flux in the upper gut of pigs. A two compartment (ileal ammonia and plasma urea) model was developed to determine possible value ranges for FAAC in the upper gut (0.0 to 13.3 ± 1.42, 15.5 ± 1.65, and 10.7 ± 1.20 mmol N/kg/d for the three treatments), but this model also has limitations. Quantifying FAAC in the upper gut of pigs offers a number of challenges, but warrants further investigation.