Parallel to fingerprinting of leukemia subclasses by gene expression profiling we propose to fingerprint leukemia subclasses using protein expression data collected by quantitative flow cytometry. A number of acute lymphoblastic leukemia subclasses with characteristic chromosomal aberrations (MLL; Bcr/Abl;E2A/PBX;TEL/AML1;hyperdiploid) have a unique gene expression profile as demonstrated by microarray studies (1-2). Among genes differentially expressed between leukemia subtypes are known proteins of which expression can be measured by quantitative flow cytometry using monoclonal antibodies (3). Here, univariate t-tests and multivariate principal component analysis (PCA) have been applied to profile phenotypes of 145 pB-ALL samples using expression data of 16 proteins. Expression of each marker protein has been quantified in terms of soluble fluorochrome (MESF) and coefficient of variation (CV). Materials:Patients material: A retrospective analysis has been performed on a total of 145 children diagnosed as suffering from precursor-B acute lymphoblastic leukemia (pB-ALL). We included 46 patients that were diagnosed for a MLL rearrangement between May 1995 and June 2001. As a control group representative of pB-ALL’s negative for MLL, we randomly selected 99 consecutively diagnosed patients from our MLL negative reference database.Among MLL patients, 26 are infants (aged < 1 year at diagnosis) and 20 non-infants while in the control group 5 infants (aged < 1 year at diagnosis) and 94 non-infants patients are present.