We compare two different isochromosomes of chromosome 20 in myelodysplastic syndromes (MDS): an isochromosome of the short arm of chromosome 20, idic(20)(q11), and an isochromosome of the long arm of a deleted chromosome 20, ider(20)(q10)del(20)(q11.2). The isochromosomes are of contrasting morphology, because opposite arms are duplicated, but they both show loss of the critical region at 20q12, as well as retention and duplication of the centromere and proximal long arm (20q11). We speculate that a region of proximal 20q is preferentially retained during deletions of the critical region in MDS and acute myeloid leukemia.