It is unknown what feeding strategy to use during chemotherapy-induced gastrointestinal mucositis, which causes weight loss and possibly malabsorption. To study the absorptive capacity of amino acids during mucositis, we determined the plasma availability of enterally administered amino acids (AA), their utilization for protein synthesis, and the preferential side of the intestine for AA uptake in rats with and without methotrexate (MTX)-induced mucositis. Four days after injection with MTX (60 mg/kg) or saline (controls), rats received a primed, continuous dual-isotope infusion (intraduodenal and intravenous) of labeled L-leucine, L-lysine, L-phenylalanine, L-threonine, and L-methionine. We collected blood samples, assessed jejunal histology, and determined labeled AA incorporation in proximal and distal small intestinal mucosa, plasma albumin, liver, and thigh muscle. MTX-induced mucositis was confirmed by histology. The median systemic availability of all AA except for leucine was similar in MTX-treated rats and in controls. However, the individual availability of all AA differed substantially within the group of MTX-treated rats, ranging from severely reduced (40% of intake in 5 of 9 rats). More AA originating from basolateral uptake than those originating from apical uptake were used for intestinal protein synthesis in MTX-treated rats (>= 420% more, P <0.05). We conclude that continuous enteral administration can enable normal AA absorption in rats with MTX-induced mucositis. The intestine prefers basolateral AA uptake to meet its need for AA for protein synthesis during mucositis. J. Nutr. 142: 1983-1990, 2012.