It is demonstrated in this report that purified E2A helix-loop-helix (HLH) proteins spontaneously form homodimers that are linked by an intermolecular disulfide bond. These homodimers bind DNA at physiological temperatures but fail to associate with either Id or MyoD. When the disulfide bond is reduced by an activity present in muscle cell lysates or disrupted by site-directed mutagenesis, the monomeric form of the protein is strongly favored at 37 degrees C. These E2A monomers cannot bind DNA but heterodimerize efficiently with Id and MyoD. It is also shown that an intermolecular disulfide bond cross-links E2A homodimers in B cells but not in muscle cells in which only heterodimers have been detected. These results suggest a novel mechanism for regulating the dimerization status and DNA binding properties of E2A HLH transcription factors.