Our objective was to determine whether neonates adapt to protein malnutrition by preserving the relative growth and metabolism of gastrointestinal tissue at the expense of skeletal muscle. We measured gastrointestinal, liver, and carcass tissue masses and blood flow, oxygen consumption, and net glucose and amino acid fluxes in vivo of the portal-drained visceral tissues (PDV) in neonatal pigs fed isocaloric diets containing either 30% protein [control (C)] or 15% [low protein (LP)] for 14 days. Relative protein mass and fasting blood flow and oxygen consumption of PDV tissue in either group were not different. Relative protein mass of liver and carcass was lower in LP pigs. Net essential amino acid absorption and insulin concentration after feeding were lower in LP pigs. Results demonstrate that protein malnutrition in neonatal pigs differentially altered rates of tissue growth, such that the proportion of body protein partitioned into gastrointestinal tissue was preserved, while that of skeletal muscle was reduced. Chronic reduction in amino acid absorption in protein-malnourished pigs resulted in a reduced insulin response to feeding, which presumably limited substrate availability and the anabolic stimulus for skeletal muscle protein accretion.