The mutation rate (m) is a key biological feature of somatic cells that determines risk for malignant transformation, and it has been exceedingly difficult to measure in human cells. For this purpose, a potential sentinel is the X-linked PIG-A gene, because its inactivation causes lack of glycosylphosphatidylinositol-linked membrane proteins. We previously found that the frequency ( f ) of PIG-A mutant cells can be measured accurately by flow cytometry, even when f is very low. Here we measure both f and m by culturing B-lymphoblastoid cell lines and first eliminating preexisting PIG-A mutants by flow sorting. After expansion in culture, the frequency of new mutants is determined by flow cytometry using antibodies specific for glycosylphosphatidylinositol-linked proteins (e.g., CD48, CD55, and CD59). The mutation rate is then calculated by the formula m = f/d, where d is the number of cell divisions occurring in culture. The mean m in cells from normal donors was 10.6 Â 10 À7 mutations per cell division (range 2.4 to 29.6 Â 10 À7 ). The mean m was elevated >30-fold in cells from patients with Fanconi anemia (P < 0.0001), and m varied widely in ataxia-telangiectasia with a mean 4-fold elevation (P = 0.002). In contrast, m was not significantly different from normal in cells from patients with Nijmegen breakage syndrome. Differences in m could not be attributed to variations in plating efficiency. The mutation rate in man can now be measured routinely in B-lymphoblastoid cell lines, and it is elevated in cancer predisposition syndromes. This system should be useful in evaluating cancer risk and in the design of preventive strategies. (Cancer Res 2005; 65(18): 8111-7)