As part of a study into the homo- and hetero-oligomerization properties of muscle-specific transcriptional factors, and their interation with DNA, sedimentation equilibrium studies, accompanied by circular dichroism measurements, have been made on peptides derived from the helix-loop-helix regions of MyoD and E47. In addition, a chimeric peptide, in which residues from the loop region of E47 were substituted into that of MyoD, a fluorescently labelled derivative of the MyoD-bHLH peptide and a disulphide crosslinked version of MyoD-bHLH have also been investigated. MyoD-bHLH has been found to form a monomer tetramer equilibrium in the µM concentration range, while E47-bHLH exists as a highly associated dimer. The MyoD-bHLH derivatives appear to exhibit the same oligomerization behavior as their MyoD-bHLH parent. CD studies of the disulphide-crosslinked peptide show that a level of organization higher than that of the dimer is required for structural stability in the MyoD-bHLH system. The role of self-association in the context of the biological function of these peoteins is discussed.