The urea cycle is responsible for the biosynthesis of urea using nitrogen atoms from amino acid catabolism, allowing the conversion of neurotoxic metabolites (ammonia derivates) into a non-toxic product, which is promptly excreted to avoid cell damage. The impairment of each one of the urea cycle enzymes causes a Urea Cycle Disorder (UCD). The general biochemical feature underlying all UCDs is the increment of plasmatic ammonia, a condition also known as hyperammonemia. Expectedly, taking into account the neurotoxic effect of ammonia, clinical signs often include behavioural and neurological abnormalities. In extreme, severe hyperammonemic coma lead to patient’s death. Ornithine Transcarbamylase Deficiency (OTCD; MIM 311250), the most common urea cycle diseases, result from reduced OTC expression/activity. The heterogeneity in enzyme expression/activity (and consequently in phenotype presentation) is a consequence of the wide mutational spectrum revealed by the OTC gene. Although being an X-linked Mendelian trait, de novo mutations are common and estimated to affect as much as 3/4 of female abnormal chromosomes. Technical advances in molecular strategies have allowed the identification of the molecular defect underlying OTCD condition. Even so, the causative mutation is not found in about 30% of the patients (unsolved cases). The reasons for such ineffective result may lie in the presence of mutations within intronic and/or regulatory regions, or to large deletions encompassing one or more exons.