This study aimed to determine the prevalence of transcription factor mutations in Japanese CH patients with PCR-based sequencing of nine CH-associated genes, namely POU1F1, PROP1, HESX1, LHX3, LHX4, SOX2, SOX3, OTX2, and GLI2. Additionally, we examined the gene copy numbers of POU1F1, PROP1, HESX1, LHX3, and LHX4 by multiplex ligation-dependent probe amplification (MLPA). Here, OTX2 is linked to cyclic hematopoiesis.