A 13-year-old boy with hypocellular primary myelodysplastic syndrome, classified as refractory cytopenia, underwent umbilical cord blood transplantation. Cytogenetic analysis revealed two rare biclonal chromosomal aberrations, del(17)(p12) and del(11)(q23). Cytogenetic analysis was a valuable tool in diagnosis, in clinical decision-making, and in treatment and follow-up. To our knowledge, this is the first reported case of cytogenetic biclonality involving chromosomes 17 and 11.