The invention provides a method for determining a dose and schedule and making dose adjustments of PBA prodrugs used to treat nitrogen retention states, or ammonia accumulation disorders, by measuring urinary excretion of phenylacetylglutamine and/or total urinary nitrogen. The invention provides methods to select an appropriate dosage of a PBA prodrug based on the patient's dietary protein intake, or based on previous treatments administered to the patient. The methods are applicable to selecting or modifying a dosing regimen for a subject receiving an orally administered ammonia scavenging drug.
