The structural proteins of polyoma virions and capsids were analyzed by isoelectric focusing and sodium dodecyl sulfate-polyacrylamide gel electrophoresis. Polyoma virion VP, was found to be composed of six distinct species which had pI's between pH 6.75 and 5.75. Polyoma capsid VP, was found to contain four species with pI's between pH 6.60 and 5.75. The different forms of virion and capsid VP, appeared to be generated by modifications (phosphorylation and acetylation) of the initial translation product. The most basic of the virion VP, species (pI, pH 6.75) was absent in capsids and was found to be exclusively associated with the viral nucleoprotein complex. Three of the virion VP, species and three of the capsid VP, species were found in capsomere preparations enriched for hexon subunits. Two VP, species were specifically immune precipitated from virions with hemagglutination-inhibiting antibodies. These two VP, species were common to both virions and capsids. Polyoma virions, but not capsids, possessed a single VP, species which was immune precipitated with neutralizing antibodies. Both virion and capsid VP2 were found to have pI's of approximately pH 5.50. Virion VP3 had a pI of approximately pH 7.00, whereas capsid VP3 had a pI of approximately pH 6.50.