The analysis of X-chromosome inactivation patterns has been used in a number of clinical situations such as the identification of carrier status in X-linked genetic disorders and the establishment of the monoclonal origin of tumors. Interpretation of the result obtained requires comparison with the constitutive pattern for the individual, and for hematopoietic malignancies, skin biopsies or cultured fibroblasts have often been used as the control tissue because normal cells of the same lineage as the malignancy are not generally available. However, this assumes that patterns in the different tissues are constitutionally the same. We have therefore compared X-chromosome inactivation patterns from peripheral blood (granulocytes, E- cells, and T cells), skin, and muscle from 20 hematologically normal females, and colonic mucosa from 9 individuals. In 11 patients (55%), the results obtained were similar for all tissues of an individual, but in 9 patients, significant differences were observed between tissues. The most consistent feature was a skewing in peripheral blood (> 75% expression of one allele) but not skin and/or muscle. These studies suggest that skin cannot be used as a control tissue for the interpretation of X-chromosome inactivation patterns in hematopoietic cells.