Hyperphenylalaninemia can result from defects in either the phenylalanine hydroxylase (PAH) enzyme or in the synthesis or recycling of the active pterin, tetrahydrobiopterin (BH4), which is an obligate co-factor for the PAH enzyme, as well as tyrosine hydroxylase and tryptophan hydroxylase. One of the most common causes of BH4 deficiency is a defect in the synthesis of 6-pyruvoyltetrahydropterin synthase (PTPS) enzyme. Patients present with progressive neurological disease such as mental retardation, convulsions and disturbance of tone and posture despite strict adherence to diet and good metabolic control. The authors report the first two cases of PTPS deficiency in the Philippines. Both are females with initial phenylalanine levels of more than 1300 umol/L who continued to develop neurologic deterioration despite good metabolic control and strict adherence to diet. Further investigation showed that they both had PTPS deficiency. Treatment was started with BH4, L-dopa/carbidopa, and 5-hydroxytryptophan (5HT) with concomitant significant improvements in their neurologic and developmental outcomes.