Deconjugation of bile salts may occur in the jejunum under conditions of bacterial proliferation in the upper small intestine. We studied the morphological changes of jejunal mucosa induced by different conjugated (taurocholate, taurodeoxycholate, taurochenodeoxycholate, tauroursodeoxycholate) and unconjugated (cholate, deoxycholate, chenodeoxycholate, ursodeoxycholate) bile salts as compared by scanning electron microscopy. The epithelial lining of the jejunum was not affected in structural appearance below 40 mM concentration of the conjugated bile salts examined. On the other hand, the unconjugated bile salts examined induced morphological changes in varying degree and severity from crack formation at the tip to complete denudation of the jejunal villi, depending on the kind and dose of bile salts given. Among the unconjugated bile salts examined, the most robust in action was deoxycholate, which induced crack formation at 1.0 mM concentration, and the weakest was cholate. The study suggests that deconjugated bile salts produced by bacterial overgrowth in the upper small intestine can induce breakdown of the junctional integrity of the epithelial lining in varying degree and severity, ultimately leading to exfoliation of the epithelium.