Abstract: Background – Bile acids (BA) aid in lipid absorption and are key microbial metabolites, acting as signaling molecules in the intestines. Serum BA are poorly characterized in dogs with chronic enteropathy (CE). Objective – Compare concurrently collected serum and fecal BA profiles between healthy control dogs (HC) and dogs with CE. Animals – 26 HC and 8 dogs with CE (all privately owned). Methods – Observational cross-sectional study. Fecal and serum concentrations of 28 BA, including unconjugated, taurine- and glycine-conjugated, and iso- and oxo-BA were measured with a previously validated LC-MS/MS method. Concentrations were compared between groups with Mann-Whitney tests. Spearman’s correlations were performed for each BA in serum and feces, adjusted by Benjamini-Hochberg procedure (FDR 5%). Results – Cholic acid and its epimer 7-oxo-deoxycholic acid were increased in serum of dogs with CE (median [min-max] ng/mL; 34 [1–74] and 1.5 [0.1–8.5]) compared to HC (8.6 [0.4–239] and 0.5 [0.1–4.5]; P< 0.04). Deoxycholic acid and its epimer 12-oxo-lithocholic acid were decreased in feces of dogs with CE (ng/mg fecal dry matter; 80 [9–5,680] and 0.5 [0–1,316]) compared to HC (4618 [45–7,501] and 527 [1–3,140]; P< 0.04). Secondary BA deoxycholic (rho=0.608, P=0.001) and hyodeoxycholic (rho=0.712, P=0.001) acids were strongly positively correlated between serum and feces. Conclusions and clinical importance – Dogs with CE had altered serum and fecal BA profiles compared to HC. Some secondary BA and their epimers are decreased and some primary BA and their epimers are increased in CE compared to HC.