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<p>Abstract</p> <p>Background</p> <p>X chromosomes are subject to dosage compensation in <it>Drosophila </it>males. Dosage compensation requires <it>cis </it>sequence features of the X chromosome that are present in both sexes by definition and <it>trans </it>acting factors that target chromatin modifying machinery to the X specifically in males. The evolution of this system could result in neutral X chromatin changes that will be apparent in females.</p> <p>Results</p> <p>We find that the general chromatin structure of female X chromosomes is distinct from autosomes. Additionally, specific histone marks associated with dosage compensation and active chromatin marks on the male X chromosome are also enriched on the X chromosomes of females, albeit to a lesser degree.</p> <p>Conclusions</p> <p>Our data indicate that X chromatin structure is fundamentally different from autosome structure in both sexes. We suggest that the differences between the X chromosomes and autosomes in females are a consequence of mechanisms that have evolved to ensure sufficient X chromosome expression in the soma of males.</p>