It is well known that some patients with monopathic thrombocytopenia in myelodysplastic syndrome (MDS) show clinico-hematologic features resembling chronic idiopathic thrombocytopenic purpura (ITP). This study examined the monoclonal nature of ITP to obtain a further insight into patients with borderline ITP and monopathic thrombocytopenia in MDS, using polymorphic trinucleotide CAG repeats in the X-linked human androgen receptor (HUMARA) gene. In this study, we separated peripheral neutrophils and mononuclear cells (MNCs) from 18 patients with chronic ITP, and analyzed them in comparison with those from normal or MDS female subjects by PCR-based HUMARA assay. All normal controls showed a polyclonal pattern of the HUMARA gene, whereas some MDS patients had monoclonality in MNC and/or neutrophils. Among ITP patients, two had a nonrandom inactivation pattern of the HUMARA gene in neutrophils, which was considered to be derived from hematopoietic cells of clonal origin, whereas no ITP patient had MNC of clonal nature. Two ITP patients with a monoclonal pattern in the neutrophil fraction were refractory to ordinary treatment. This approach may provide further information in patients with borderline hematologic disorders between chronic ITP and refractory thrombocytopenia of MDS.