Transcription of the calcitonin (CT) gene in the medullary thyroid carcinoma (MTC) cell line TT is modulated by a neuroendocrine-specific enhancer fragment (nucleotides -965 to -905) containing two CANNTG motifs (E2 and E3) and an ETs-like response element. To determine the cell-specific component of this fragment, oligonucleotides containing the individual elements were inserted in front of a minimal CT promoter and tested for reporter protein production in CT-positive (TT) and -negative (RO-D81 and HeLa) cells. In TT cells, using two copies of E2 or four copies of Ets increased minimal promoter activity a 20-40 fold. Using two copies of E3 had no effect on minimal promoter activity. In CT-negative MTC cells (RO-D81), the Ets response element was active but the two copies of E2 were not. Similar results were obtained with the non-neuroendocrine cell-line HeLa. I therefore concluded that E2 was the cell-type-specific component of the enhancer. An E2-specific binding protein was detected in both MTC cell lines but not in HeLa. This protein had different mobility and DNA-binding specificity in CT-positive TT cells and CT-negative RO-D81 cells. In conclusion, the CAGCTG motif of E2 modulated the cell-specific transcription of the CT gene, and its inactivation in CT-negative MTC cells correlated with modifications in its binding proteins.