Optimized whole-blood assay for measurement of ZAP-70 protein expression chronic lymphocytic leukemia (CLL) is characterized by a clonal expansion of small lymphocytes commonly expressing cell surface markers (CD5 and CD19) that are consistent with a population of B lymphocytes. While CLL can be relatively indolent, in some individuals it can progress rapidly into a life-threatening disease. A number of different markers have been proposed as useful in predicting the disease course (Binet et al., 2006). Although ZAP-70 protein expression has been correlated with the disease course Orchard et al., 2004;Rassenti et al., 2004;Del Giudice et al., 2005;Schroers et al., 2005;Krober et al., 2006), there is currently no agreement on a uniform methodology, reagents, or data-analysis techniques to perform a clinically useful measurement of ZAP-70 protein expression using flow cytometry.Using modifications to a recently published technique that was developed to fix and permeabilize whole-blood samples for measurement of intracellular signal-transduction proteins (Chow et al., 2005), the authors have developed a technique to measure ZAP-70 protein levels in whole-blood samples. The protocols used here include: (1) an optimized fixation/permeabilization technique that allows labeling of cell surface markers and intracellular ZAP-70 protein with significantly greater signal-to-noise ratio (SNR) compared to other reported fix/perm methods, (2) an optimized combination of antibodiesfluorophores to maximize ZAP-70 expression levels, (3) standardized methodology to set up flow cytometers, including compensation, to improve inter-and intra-laboratory reproducibility, and (4) a method to index ZAP-70 protein expression levels to internal positive and negative cell populations (see Shankey et al., 2006). This protocol describes a technique to measure ZAP-70 protein expression in wholeblood specimens from CLL samples. It includes the use of cell surface-specific antibodies essential for the identification of key cell populations in the sample, including the residual normal T and B cells, which are used as internal positive and negative controls. These are used to index ZAP-70 protein expression levels in the CLL population. The Basic Protocol is designed for a flow cytometer equipped with a single (488-nm) laser.An important strength of this optimized assay is the use of standardized instrumentation and compensation set up. This enhances the ability to perform ZAP-70 measurements in a reproducible manner, both within a laboratory and among different laboratories. The use of calibrated bead standards to normalize fluorescence intensities for each fluorescence channel allows standardization and reproducible results when using the same or multiple instruments. This is particularly important when trying to standardize results from different laboratories. It should be noted that the protocol described here is specific for use with a particular flow cytometer (FC-500, Beckman Coulter, Inc.). However, a similar approach should be used regard...