A mathematical model is presented that compartmentalizes endogenous secretions into the gastro-intestinal tract, according to site of origin. This model was applied to data from three growing lambs (initial liveweight 25-30 kg) given a daily dose of 2500 Trichostrongylus colubriformis larvae for 12 weeks. At weeks 0, 6 and 12 of infection, endogenous leucine flows were determined during an 8 d intra-jugular infusion of [1-¹³C]leucine, with samples taken from the jejunum, ileum and plasma. The infection had no effect on jejunal leucine flow (102.1 vs 105.5 mmol/d), but ileal leucine flow increased from 18.6 to 26.3 mmol/d (P=0.023). Endogenous leucine flow at the jejunum was unaffected by the infection (15.0 vs 18.9 mmol/d; P=0.116) but was doubled at the ileum (5.5 vs 10.4 mmol/d; P=0.025). Secretions into the small intestine contributed 58 (controls) to 65% (parasites) of ileal endogenous flow. The model also predicted that net portal drained viscera appearance was, at maximum, 79% of net appearance in the mesenteric vein.