We have used antibodies directed against two histone H2a variants, H2a.1 and H2a.2, to probe chromatin structure in Friend erythroleukemia cells. Each molecule has at least one unique antigenic determinant, as well as determinants shared by both variants. Some Friend leukemia cell types contained H2a molecules which showed altered immunologic reactivity with the two antisera. The accessibility of the H2a variants in chromatin to anti-H2a antibody was different as measured by the use of whole chromatin as an immunoabsorbent and by binding of antibody to nucleosomes in a solid phase radioimmunoassay. While anti-H2a.1 IgG bound to chromatin, anti-H2a.2 IgG did not. Moreover, anti-H2a.1 IgG binding to chromatin from different Friend cell types reflected, in general, the relative amounts of H2a.1 in total chromatin. The different reactivity of the two antisera with chromatin was also observed with isolated nucleosomes: anti-H2a.1 IgG bound but anti-H2a.2 did not. Furthermore, the binding of anti-H2a.1 Ig with subfractions of nucleosomes varied; H1-depleted, high mobility group-enriched nucleosomes reacted better than H1-containing, high mobility group-depleted nucleosomes. These findings demonstrated a heterogeneity in the organization of H2a variants in chromatin within nucleosomal subfractions of chromatin and among chromatin of different Friend leukemia cell types. Moreover, most of the antigenic determinants common to both H2a variants were shown to be buried within the nucleosome core; only H2a.1-unique determinants were accessible to an anti-H2a.1 IgG molecule.