The proteins which compose the complex of dystrophin and its associated proteins were analyzed by two-dimensional PAGE, i.e., electrofocusing in the presence of 8 M urea followed by SDS PAGE. Silver-staining of the gel showed many more spots than were expected from the results of one-dimensional SDS PAGE. By examination of their reactivity with specific antibodies, various lectins and 3-(trifluoromethyl)-3-(m-[125I]iodophenyl)-diazirine, most of these spots were identified as dystrophin and its associated proteins described previously. Several as yet unidentified minor proteins were also detected. Dystrophin-associated protein A1 was separated into two groups, alpha-A1 and beta-A1, both composed of numerous spots. These groups differed from each other in isoelectric point, molecular mass, and reactivity with antibodies. The beta-A1 group (64 kDa) was more basic than the alpha-A1 group (60 kDa). Beta-A1 but not alpha-A1 reacted with several lectins, indicating that beta-A1 is a glycoprotein. This is incompatible with the report that 59DAG, which corresponds to A1 (alpha-A1 + beta-A1), is not a glycoprotein [Ervasti et al. (1991) Cell 66, 1121-1131]. The charge heterogeneity observed in alpha-A1 and beta-A1 may be partially due to differential phosphorylation. The charge heterogeneity of A2 and A3a may, at least to some extent, be due to differential sialilation of their carbohydrates.