X chromosome structural abnormalities are relatively common in Turner syndrome patients, in particular X isochromosomes. Reports over the last five decades examining asynchronous DNA replication between the normal X and isochromosome have clearly established that the structurally abnormal chromosome is the inactive X chromosome (Xi). Here the organization of chromatin at a deleted X chromosome, an Xq isochromosome, and two isodicentric chromosomes were examined. Consistent with previous differential staining methods, at interphase, the X isochromosome and isodicentric X chromosomes frequently formed bipartite Barr bodies, observed by fluorescence microscopy using numerous independent bona fide markers of Xi heterochromatin. At metaphase, with the exception of the pseudoautosomal region and the duplicated locus of the macrosatellite DXZ4 (if present on the abnormal X chromosome based on break points), euchromatin markers were absent from the Xi, whereas histone variant macroH2A formed reproducible banded mirror-image chromosomes. Unexpectedly, the isodicentric chromosome in 46,X,idic(X)(q28) cells, which carry a near full-length q-arm-to-q-arm fused chromosome, showed at interphase very rare instances of Xi chromatin bodies that were separated by large distances in the nucleus. Further examination using immunofluorescence and FISH support the possibility that these rare cells may represent ones in which one half of the isodicentric chromosome is active and the other half is inactive.