Biochemicals in the upper-gut aspirate in 31 patients with malabsorption syndrome (MAS) with and without small intestinal bacterial overgrowth (SIBO), and 10 disease-free controls were analyzed using high-resolution (1)H-NMR spectroscopy, and were correlated with the degree of SIBO and severity of MAS. Compared to controls, the patients had higher quantities (micromol/L: median [range]) of total bile acids/cholesterol (2000 [0-12000] vs. 300 [0-600]), lactate (700 [0-5200] vs. nil [0-30]), acetate (200 [0-6500] vs. 20 [0-200]), and formate (80 [0-900] vs. nil [0-50]) (P < 0.01, Mann-Whitney U-test). However, amino acids and glucose were comparable in both. Quantities (micromol/L: median [range]) of acetate (1330 [220-6500] vs. 100 [0-1430]), lactate (1430 [670-3300] vs. 300 [0-5200]), formate (360 [0-600] vs. 25 [0-800]), and unconjugated bile acids (500 [40-600] vs. 10 [0-300]) were higher in MAS patients with SIBO than those without SIBO (P < 0.01, Mann-Whitney U-test, for all). In patients with MAS the quantity of acetate positively correlated with the degree of SIBO, and unconjugated bile acids correlated with the degree of steatorrhoea (Spearman's rank correlation coefficient, two-tailed, P < 0.05: 0.46 and 0.52, respectively). This study demonstrates the bacterial production of metabolites and deconjugation of bile acids in patients with MAS.