While there is evidence that the two ubiquitously expressed thyroid hormone (T3) receptors, TR alpha 1 and TR beta 1, have distinct functional specificities, the mechanism by which they discriminate potential target genes remains largely unexplained. In this study, we demonstrate that the thyroid hormone response elements (TRE) from the malic enzyme and myelin basic protein genes (METRE and MBPTRE) respectively, are not functionally equivalent. The METRE which is a direct repeat motif with a 4-base pair gap between the two half-site hexamers binds thyroid hormone receptor as a heterodimer with 9-cis-retinoic acid receptor (RXR) and mediates a high T3-dependent activation in response to TR alpha 1 or TR beta 1 in NIH3T3 cells. In contrast, the MBPTRE, which consists of an inverted palindrome formed by two hexamers spaced by 6 base pairs, confers an efficient transactivation by TR beta 1 but a poor transactivation by TR alpha 1, While both receptors form heterodimers with RXR on MBPTRE the poor transactivation by TR alpha 1 correlates also with its ability to bind efficiently as a monomer, This monomer, which is only observed with TR alpha 1 bound to MBPTRE, interacts neither with N-CoR nor with SEC-I, explaining its functional inefficacy, However, in Xenopus oocytes, in which RXR proteins are not detectable, the transactivation mediated by TR alpha 1 and TR beta 1 is equivalent and independent of a RXR supply, raising the question of the identity of the thyroid hormone receptor partner in these cells. Thus, in mammalian cells, the binding characteristics of TR alpha 1 to MBPTRE (i.e. high monomer binding efficiency and low transactivation activity) might explain the particular pattern of T3 responsiveness of MBP gene expression during central nervous system development.