We previously reported that our patients with congenital primary hypothyroidism associated with thyrotropin (TSH) unresponsiveness through an autosomal recessive pattern of inheritance did not have mutations in the coding region of the TSH receptor gene. In the current study, we analyzed the promoter of the TSH receptor gene and the entire region of the thyroid transcription factor-1 (TTF-1) gene, including promoter, two exons, and one intron, because expression of the rat TSH receptor gene is reported to be stimulated by the interaction of the promoter of the TSH receptor gene with TTF-1. Screening for mutations was performed by RNase cleavage assay, and the polymerase chain reaction (PCR) products were subsequently sequenced by the automatic sequencer. In the promoter of the TSH receptor gene, a duplication of nucleotides -346 to -330 was detected in one allele, but haplotype analysis of the family demonstrated lack of linkage between the duplication and the TSH unresponsiveness. The same duplication was also observed in some normal subjects. In the TTF-1 gene, we detected a transition (guanine to adenine) in the intron at the minus four position of cryptic 3' splice site in one allele, but absence of linkage suggested that the transition was not responsible for the TSH unresponsiveness. The same transition also was found in some normal subjects. These results suggest that TSH unresponsiveness in our patients is unlikely to be caused by mutations either in the promoter of the TSH receptor gene or in the TTF-1 gene.