We report a patient with primary myelodysplastic syndrome (MDS) and two coexisting karyotypically independent clones. Cytogenetic investigation of bone marrow (BM) cells at diagnosis showed, besides the cells with normal karyotype, a clone that manifests an interstitial deletion of the long arm of chromosome 5 and a second one with a t(5;17). The rarity of finding a BM mosaicism in myelodysplasia with 5q- in some cells and different chromosomal abnormalities in others may be considered to support the multistep theory of pathogenesis in MDS.