In clonality assays using X chromosome inactivation patterns (XCIPs), several factors such as constitutive and acquired XCIP skewing, lack of appropriate controls for hematopoietic diseases including multilineage disorders, and ambiguous criteria for monoclonality, have complicated determination of clonality. To address these issues, we studied the significance of the buccal epithelium as a non-hematopoietic control and the usefulness of the 95% rejection limit as a criterion for monoclonality. Sixty-nine females informative for human androgen receptor gene (HUMARA) were divided into "young," "middle-aged" and "elderly" groups. When XCIP correlation between the buccal epithelium, peripheral granulocytes, and peripheral lymphocytes was analyzed, the buccal epithelium showed a good correlation with granulocytes and lymphocytes in "young" and "middle-aged" groups, whereas the correlation was poor for the "elderly" group. For all age groups, there was an excellent correlation between granulocytes and lymphocytes. When we performed clonality assay for seven "young" and "middle-aged" patients with various leukemic phases using buccal epithelium as a non-hematopoietic control, all cases were accurately evaluated with the aid of a novel criterion, the 95% rejection limit. Our findings suggest that the buccal epithelium may constitute an effective control, especially when a non-hematopoietic control is required, and that the 95% rejection limit may serve as a statistically-defined criterion for monoclonality.