Regulation of the thyroid transcription factor-1 (TTF-1) gene expression in the thyroid was investigated. We identified a new transcription start site as nucleotide (nt) -1917, 1700 bp upstream of previously described site, and the region encompassing nt -1242 to -14 as the first intron. Although a probe targeting exon 2 hybridized to both 3.7 and 2.7 kp transcripts, a probe targeting newly identified exon 1 mainly reacted with 3.7 kb transcript, indicating that there exsits a transcript from -1917. Chloramphenicol acetyltransferase (CAT) reporter gene assays demonstrated that 5'-flanking region of the start site exhibited promoter activity in FRTL-5 cells but not in rat liver cells, suggesting that this region confers the thyrocyte-selective expression of the gene. Two consensus TTF-1 binding motifs were detected in this promoter region, and electrophoretic mobility-shift assays showed that oligonucleotide probes, each containing one of these motifs, formed a complex with the recombinant TTF-1 homeodomain. Moreover, recombinant TTF-1 increased the transcriptional activity in FRT cells which do not express TTF-1. These results suggest that transcription from the newly identified start site in the TTF-1 gene is positively regulated by TTF-1 in the thyroid.