For routine evaluation of the quality of dietary protein, amino acid scoring patterns were used. Evaluation of this pattern for soy and casein revealed that these proteins are of almost equal quality. However, in vivo studies showed a large difference. To study the biological effects of meals with casein and soy protein, the contributions of individual amino acids to net protein retention and amino acid kinetics in gut, liver and muscle in healthy pigs were investigated. Isonitrogenous enteral nutrition, infused at a rate of 10 mL ⋅ kg body wt−1 ⋅ h−1 and consisting of maltodextrin (137 g/L) with added casein (53 g/L) or soy protein (68 g/L), was given to conscious, healthy female multicathetized pigs (20–22 kg, n = 12). A primed-constant infusion protocol with L-[ring-2,6-3H]phenylalanine, L-[3,4-3H]valine and [15N-15N]urea was used to measure amino acid and urea kinetics in gut, liver and muscle. Measurements were done postabsorptively and 2–6 h after initiation of the enteral nutrition. During the meal, appearance of amino acids into the portal vein and the uptake by the liver was lower with casein infusion. Muscle uptake did not differ. Gut protein synthesis tended to be lower with soy infusion (P = 0.1). Liver protein synthesis and degradation were higher with casein infusion (P < 0.05), while in muscle, soy infusion stimulated protein turnover (P < 0.05). In comparison to the postabsorptive condition, liver urea production was unchanged after casein infusion, while it was significantly increased after soy infusion. These results suggest that the quality of soy protein is inferior to that of casein protein.