Experiments with biosynthetic incorporation of 3H-amino acids into murine and guinea pig Ia antigens have indicated that these antigens consist of two polypeptide chains of 33,000 and 25,000 daltons, respectively, occasionally linked by disulfide bonds into a 58,000 dalton molecule. In contrast, studies with lactoperoxidase-catalyzed radioiodination have indicated that these Ia antigens consist of only a single chain of 25,000 daltons. We therefore undertook a study to explore the basis of these discrepant results. Since 3H-tyrosine labeled both chains well, the lack of tyrosine residues in the 33,000 dalton chain could not be the explanation for the lack of radioiodination. However, by partially purifying the Ia antigen preparation with Lens culinaris (lentil) lectin affinity chromatography before immunoprecipitation and by increasing the resolution of analysis by using discontinuous-SDS polyacrylamide gel electrophoresis, it was possible to show that the 33,000 dalton chain was in fact radioiodinated, though still poorly so relative to the 25,000 dalton chain, and that a radioiodinated 58,000 dalton molecule could be detected. These experiments suggest that the 25,000 dalton chain is more exposed to the external cellular environment, and thus more readily iodinated by lactoperoxidase. In addition, the studies indicate that the choice of labeling method, purification procedures, and analytical methods must be taken into account when interpreting experimental results.