Background: Linker histones are functionally heterogeneous. Results: Using a novel FRAP approach, the N-terminal domain modulates binding affinities of H1 0 and H1c; the C-terminal domain influences the nucleosomal orientation of the globular domain. Conclusion:The variable terminal domains have distinct roles in the chromatin binding characteristics of linker histones. Significance: Evidence for a structural basis for the functional heterogeneity of linker histones is presented.