Allan-Herndon-Dudley syndrome (AHDS) is a neurodevelopmental disorder that manifests as intellectual disability and motor developmental delay. Thyroid hormone transporter dysfunction due to SLC16A2 mutation is the underlying cause of this disorder. We identified a novel (P537del) and a recurrent (A150V) SLC16A2 mutation in Japanese AHDS patients from two different families. A150V co-segregated with S33P. Both patients showed similar clinical features including severe neurological features and delayed myelination. Thyroid function showed a common finding of elevated T3 levels. No clear genotype-phenotype correlation was observed in patients with SLC16A2 alterations.