Portal-systemic shunting in rats results in altered plasma concentrations of the large neutral amino acids (NAA), and increased blood-brain barrier NAA transport. Bacterial ammonia production in the bowel, especially the colon, is thought to play a major role in the etiology of portal-systemic encephalopathy (PSE). In order to isolate the role of bacteria in PSE, plasma and brain amino acids and ammonia (NH 3) were studied in germ-free (GF) rats with portacaval shunts (PCS). Germ-free rats underwent end-to-side portacaval shunt or sham operation under germ-free conditions and were kept in a germ-free isolator under careful bacteriologic control. Similar operations were carried out on conventional animals. Two weeks post-operatively blood-brain transport of the neutral amino acid tryptophan was studied and the animals sacrificed. Plasma NH 3 rose after PCS both in GF and in conventional rats. In germ-free and conventional rats with PCS, there was a significant elevation in plasma of the aromatic amino acids and decreased concentrations of the branched-chain amino acids. In the brain, both groups had elevated aromatic amino acids, while the branched-chain amino acids remained normal. The blood-brain transport of tryptophan was elevated in portacaval shunted rats, whether germ-free or conventional. These studies suggest the elevated plasma levels of ammonia and disturbances in plasma and brain amino acids seen after portacaval shunt are not dependent on the presence of gut bacteria.