Conflicting results have been published on the frequency of clonal patterns of X-chromosome inactivation in female patients with aplastic anaemia. Previous studies have used DNA methylation to measure X-inactivation, but aberrant methylation is known to occur in some situations. We have developed a non-radioactive reverse transcription polymerase chain reaction (RT-PCR) method to study expression of the polymorphism at nt. 1311 of the G6PD gene at the RNA level. Using this, and a similar method for the iduronate-2-sulfatase (IDS) gene, we have re-evaluated X-inactivation in AA patients. 32/35 normal individuals showed polyclonal haemopoiesis. Patients with presumed clonal diseases showed both monoclonal and polyclonal patterns, consistent with previous reports. Overall, clonal patterns were observed in granulocytes of 10/26 AA patients (38%), a significantly higher proportion than in controls (p<0.01). Two cases showed discordance between lymphocytes and granulocytes, indicating clonality arising within the myeloid lineage. Eight cases showed clonal patterns in both myeloid and lymphoid cells, indicating the involvement of a pluripotent stem cell. Clonal patterns did not correlate with age, but there appeared to be an association with duration of disease. In PNH patients, CD59-negative cells showed clonal patterns of X-inactivation. In two cases, however, clonal patterns were also detected in CD59-positive cells.