Ornithine transcarbamylase (OTCase) was purified from the small intestine of rat and the properties of the gut enzyme were compared with those of the enzyme from liver. The enzymes from both sources bound to the transition-state analog inhibitor, delta-N-(phosphonoacetyl)-L-ornithine, immobilized on Sepharose and eluted with carbamyl phosphate as a homogeneous preparation. The specific activities of the pure enzymes were 966 mumol min-1 mg-1 and 928 mumol min-1 mg-1 from liver and gut respectively, and the molecular mass, based on electrophoretic mobility, was 38 000 Da. The isoelectric point of the enzymes from both sources was 7.3. The enzymes from both sources cross-react to the same extent with antibodies against the liver enzyme on Western transfers and the size of the mRNA was identical on Northern transfers probed with a cDNA for the liver enzyme. Although OTCase is apparently the same gene product in both liver and gut, the enzyme levels respond differently to alterations in the protein content of the diet. OTCase in liver increased from 0.76 mumol min-1 microgram-1 DNA on 15% casein to 1.3 mumol min-1 microgram-1 DNA on 60% casein (P less than 0.01) whereas in small intestine the level decreased from 8.8 nmol min-1 microgram DNA on 15% casein to 5.7 nmol min-1 microgram-1 DNA on 60% casein (P less than 0.05). When expressed on a fresh-weight basis, the enzyme activity in liver shows the characteristic increase with increasing protein, whereas the activity in gut does not. The connection between these differences in gene expression and the different physiological roles of OTCase in liver and gut is discussed.