Peptides of hexons from type 2 and 5 (subgroup III) and type 3 (subgroup I) adenoviruses were produced by treatment with cvanogen bromide and were separated by isoelectric focusing in polyacrylamide gels containing 8 M urea. Peptides with identical isoelectric points, but from different hexon types, were considered to have structural similarities. According to this criterion for chemical relatedness, about two-thirds of the type 2 and 5 hexon peptides may be considered similar. In contrast, the majority of the type 3 hexon peptides differed chemically from peptides of' type 2 and 5 hexons. Virions and free hexons were iodinated with 1251 in the presence of lactoperoxidase and H202. When 125J1 labeled virions were disrupted and the hexon was purif'ied, the highly labeled cyanogen bromide peptides had pl values greater than 6.8; some unique as well as some common peptides were labeled. When purif'ied hexons from the excess cellular pool were iodinated, peptides common to types 2, 3, and 5 (peptides 12 and 14) were most extensively labeled. Thus, hexons assembled in virions and those free in solution were iodinated differently. The data suggest that immunologically the hexons in viral capsids react dif'ferently from unassembled hexons because the polypeptide chains assume slightly different f'olding configurations in the two hexon forms and therefore expose dif'ferent regions of' the protein to antibodies.