It is now the most frequent inborn error of the urea cycle. Some of these features are illustrated in the attached DVD of the index patient, then twenty months old, being examined by one of the authors of the two papers first describing the syndrome. OTC deficiency presents in different ways neurologically and with different degrees of severity. The index patient was severely affected and it is suggested that the very marked muscular tonus illustrated is caused by the effect of ammonia on spinal reflexes. Ornithine transcarbamylase (OTC) deficiency is an X-linked urea cycle disorder affecting both sexes. We describe a large pedigree with OTC deficiency. A 15 months old girl was hospitalised with vomiting, poor appetite and lethargy. Elevated liver enzymes, lactic acid and ammonia (210 μmol/l) were found in blood. Glutamine in plasma was slightly elevated, otherwise aminoacids in plasma and urine were normal, orotic acid in urine also was normal. In anamnesis one of patient's sisters died suddenly at the age of 5 years with Rey syndrome, coma, encephalopathy. Another sister was strongly vegetarian. The mother's two brothers died in the neonatal period. The patient's niece died at the age of 11 months after viral respiratory disease with rapid coma and brain death and three cousins died in second and third day of life with respiratory problems, seizures, coma. Ammonia levels were not examined. OTC deficiency was suspected in our patient and the finding of the R142Q/N mutation in the OTC gene confirmed the diagnosis. The same mutation was found in the patient's mother, sister and in postmortem material in one of the deceased cousins. Our report shows the importance of early checking of ammonia in all patients with acute encephalopathy, coma. Residual phenylalanine hydroxylase (PAH) activity is the key determinant for the phenotype severity in phenylketonuria (PKU) patients and is reported to correlate with the genotype. Activity of in vitro expressed recombinant mutant PAH proteins may predict the patient's phenotype and pharmacological response to tetrahydrobiopterin (BH4). We developed a PAH assay using a LC-MS/MS method for quantitative determination of phenylalanine and tyrosine after derivatization with Phenomenex EZ:faast kit. Several frequent PAH mutations (R158Q, R261Q, R408W, I65T) were expressed in eukaryotic COS-1 cells and quantified for PAH activity. In addition, PAH activity was measured in several cell lines (Huh-7, Hep3B) as well as in liver, brain, and kidney tissue from wild-type and PKU mice. The PAH assay is linear for both amino acids, phenylalanine as well as tyrosine (r2 ≥0.99) and exhibits a low limit of detection of less than 200 nmol/L. In addition the method allows differentiation of endogenous and enzymatically produced tyrosine in cell extracts. Intra-day coefficients of variance (CV) were less than 2.7% and inter-day CV less than 5.7% in lower tyrosine range. The accuracy determined through recovery was 105%. In conclusion, quantification of phenylalanine and tyrosine by LC-MS/MS is highly specific, reproducible, and faster than previously used methods. High variability in blood phenylalanine (phe) levels have been shown to be related to a poorer cognitive outcome in individuals with phenylketonuria (PKU) suggesting that intermittently high (or low) levels may have a deleterious effect in addition to that associated with high average blood phe concentrations.