Pediatric neurotransmitter disease (PND) encompasses a range of rare genetic disorders that affect the metabolism of neurotransmitters in children. While these neurological disorders are often studied independently of each other, they all manifest central nervous system symptoms and require proper diagnosis and intervention at early stages. Since clinical symptoms of PND can be nonspecific, the conditions are often under-diagnosed, leaving patients without a chance to receive effective treatment. Envisioning PND as a whole, a comprehensive research effort is underway for a better understanding of pathophysiology and epidemiology in Japan, and toward the establishment of diagnostic criteria. The early diagnosis and development of new effective therapies are of urgent importance for these rare disorders that are not covered by newborn mass screening. For rarer forms of PND, at the same time, it is important to encourage recognition and understanding of the disease concept among healthcare professionals.