Urea cycle disorders (UCDs) result from inherited defects in the ammonia detoxification pathway, leading to episodes of hyperammonaemia and encephalopathy. The purpose of this study was to answer the question, "what is the likely plasma amino acid profile of a patient known to have a UCD presenting with hyperammonaemia during acute metabolic decompensation", in order to support informed decisions regarding management.We analysed the results of plasma ammonia levels and amino acid profiles taken simultaneously or within 30 min of each other during acute admissions of all patients with a UCD at the Royal Children's Hospital, Melbourne, over 28 years. Samples from 96 admissions (79, 9 and 8 admissions for OTC, CPS and ASS deficiencies, respectively) from 14 patients fulfilled these criteria. Amino acid levels were measured by ion exchange chromatography with post-column ninhydrin derivatisation and interpreted in relation to age-related reference ranges.Plasma concentrations of all measured essential amino acids were low or low-normal in almost all samples. There was a strong positive correlation between low plasma branched-chain amino acids and other essential amino acids, and a negative correlation between ammonia and phenylalanine to tyrosine (Phe:Tyr) ratio in patients with OTC deficiency, and between glutamine and Phe:Tyr ratio in all patients, indicating protein deficiency.Conclusion: At admission, protein deficiency is common in patients with a UCD with hyperammonaemia. These results challenge the current guideline of stopping protein intake during acute decompensation in UCDs. Supplementation with essential amino acids (particularly branched-chain amino acids) at these times should be considered.