Thyroid hormone (triiodothyronine, T3) is known to activate transcription by binding to heterodimers of thyroid hormone receptors (TRs) and retinoid X receptors (RXRs). RXR-TRs bind preferentially to T3 response elements (TREs) comprised of direct repeats of the sequence AGGTCA spaced by four nucleotides (DR-4). In other TREs, however, the AGGTCA half-sites can be arranged as inverted palindromes (IP) and palindromes (pal). Here, we present evidence that TR homodimers and monomers activate transcription from representative TREs with alternate half-site placements. We find that TRb activates transcription more efficiently than TRa at an IP element (F2) and that this correlates with preferential TRb homodimer formation at F2 in vitro. Further, reconstruction of TR transcription complexes in yeast indicates that TRb homodimers are active at F2 whereas RXR-TRs are active at DR-4 and Pal. Finally, analysis of effects of TRb mutations that block homodimer and/or heterodimer formation reveals TRE-selective requirements for these surfaces in mammalian cells which suggest that TRb homodimers are active at F2, RXR-TRs at DR-4 and TR monomers at Pal. TRb requires higher levels of hormone for activation at F2 than other TREs and this differential effect is abolished by an LBD dimer surface mutation suggesting that it is related to the composition of the TR/TRE complex. We propose that interactions of particular TR oligomers with different elements play an unappreciated role in TRE-selective actions of liganded TRs in vivo.