Methods of diagnosing Crohn’s disease and ulcerative colitis in subjects is provided based on the determination of metabolites in urine samples, such as serine, hypoxanthine, kynurenine, threonine, dimethylglycine, tryptophan, indoxylsul-fate, phenylacetylglutamine, sialic acid, 5-hydroxy-6-indolyl-o-sulfate, 5-(Δ-carboxybutyl) homocysteine, and/or an anion having m/ z:RMT:polarity of 345.1553:0.770:n, or determination of metabolites in stool samples, such as ketodeoxycholic acid, cholic acid, choline, tryptophan, trimethyllysine, serine, butyric acid, lactic acid, hypoxanthine and/or guanine.