Sensitive and specific radiochromatographic methods to measure enzymatic activities of carbamyl phosphate synthetase I (CPS I) and ornithine transcarbamylase (OTC) were developed. The activities of these enzymes were assayed in frozen liver tissue obtained from 23 individuals with hyperammonemia caused by CPS I (five patients) and OTC deficiency (18 patients). In addition, livers of one aborted fetus with OTC deficiency and four normal individuals were studied. The assays use radioactive ornithine as a substrate followed by separation of citrulline formed in the reactions by HPLC and quantitation of the radioactivity in both aminoacids by a radioactivity flow monitor or by a scintillation counter. Both CPS I and OTC assays were linear with respect to length of incubation time and concentration of tissue homogenate. The sensitivity of the methods allowed measurements of CPS I and OTC activities as low as 0.1 μmol/g/min on 5 mg of liver tissue and the diagnosis of CPS I or OTC deficiency could be established on as low as 0.5 and 0.05 mg of tissue, respectively. CPS I activity in different sections of four normal livers was 3.01 ± 0.16 μmol/g/min (mean ± SEM, n = 19) and OTC activity was 93.4 ± 6.3 (mean ± SEM, n = 19). Residual enzymatic activity could be detected and measured in the liver tissues of one of the five subjects with CPS I deficiency and in 14 of 19 subjects with OTC deficiency. OTC/CPS I activity ratio in normal liver tissue was 31.2 ± 1.3 (mean ± SEM, n 19), whereas this ratio ranged from 343 to >5000 in CPS I deficient livers and from <0.02 to 1.55 in OTC deficient livers. The OTC/CPS I ratio was found to be a reliable parameter for assessing enzymatic deficiency compensating for the observed variability of enzymatic activity between individual samples. OTC/CPS I ratio also seemed to correlate with the severity of disease in enzyme deficient patients. OTC-deficient patients with the highest residual enzymatic activity (1-3% of normal) had a better outcome. These sensitive methods would help to establish the diagnosis of CPS I or OTC deficiency whenever only a very small amount of liver tissue is available and their results could be interpreted even if secondary reduction in the activities of these enzymes occurred due to collection or storage artifacts. Levels of residual enzymatic activities may help to predict the prognosis of these patients.