We recently showed that the developing gut is a significant site of methionine (Met) transmethylation to homocysteine and transsulfuration to cysteine (Cys). We hypothesized that sulfur amino acid (SAA) deficiency would preferentially reduce mucosal growth and antioxidant function in neonatal piglets. Neonatal pigs were enterally-fed a control diet or SAA-free diet for 7 d and then whole-body methionine and cysteine kinetics were measured using an intravenous infusion of [1-¹³C;methyl-²H₃]-Met and ¹⁵N-Cys. Body weight gain and plasma Met, Cys, homocysteine, taurine and total erythrocyte glutathione concentrations were markedly decreased (-46 to -85%) in SAA-free vs. control pigs. Whole-body Met and Cys fluxes were reduced, yet Met utilization for protein synthesis and Met remethylation were relatively preserved at the expense of Met transsulfuration in response to SAA-deficiency. Intestinal tissue concentrations of Met and Cys were markedly reduced and hepatic levels were maintained in SAA-free pigs vs. control pigs. SAA-deficiency increased the activity of methionine metabolic enzymes, i.e. methionine adenosyltransferase (MAT), methionine synthase (MS) and cystathionine -synthase (CBS), and SAM concentration in the jejunum, whereas MS activity increased and SAM level decreased in liver. Small intestine weight and protein and DNA mass were lower, whereas liver weight and DNA mass were unchanged in SAA-free pigs compared to control pigs. Dietary SAA-deficiency induced small intestinal villus atrophy, lower goblet cell numbers and Ki-67-positive proliferative crypt cells in association with lower tissue glutathione, especially in the jejunum. We conclude that SAA-deficiency upregulates intestinal methionine cycle activity and suppresses epithelial growth in neonatal pigs.