X-linked agammaglobulinemia (XLA) is a rare disorder in which recurrent infections occur due to low serum globulins and circulating B lymphocytes caused by a mutation in the Bruton tyrosine kinase (Btk) gene. While myelodysplastic syndrome (MDS) associated with low B lymphocyte counts has been described, clonal cytogenetic abnormalities in confirmed cases of XLA have never been reported. We describe a case of XLA with a novel Btk mutation who also had a persistent clonal population in the bone marrow with abnormal cytogenetics in multiple chromosomes that resolved 1½ years after treatment with IVIG, mimicking a picture of transient MDS. Pediatr Blood Cancer 2008;51:826–828. © 2008 Wiley-Liss, Inc.