A procedure is presented for calibrating the output of a multicolor flow cytometer in units of antibodies bound per cell (ABC). The procedure involves two steps. First, each of the fluorescence channels of the flow cytometer is calibrated using Ultra Rainbow beads with assigned values of equivalent number of reference fluorophores (ERF). The objective of this step is to establish a linear relation between the fluorescence signal in a given fluorescence channel of multicolor flow cytometers and the value of ERF. The second step involves a biological standard such as a lymphocyte with a known number of antibody binding sites (e.g., CD4 binding sites). The biological standard is incubated with antibodies labeled with one type of fluorophores for a particular fluorescence channel and serves to translate the ERF scale to an ABC scale. A significant part of the two-step calibration procedure involves the assignment of ERF values to the different populations of Ultra Rainbow beads. The assignment of ERF values quantifies the relative amount of embedded fluorophore mixture in each bead population. It is crucial to insure that the fluorescence signal in a given range of fluorescence emission wavelengths is related linearly to the assigned values of ERF. The biological standard has to posses a known number of binding sites for a given antibody. In addition, this antibody has to be amenable to labeling with different types of fluorophores associated with various fluorescence channels. The present work suggests that all of the requirements for a successful calibration of a multicolor flow cytometer in terms of ABC values can be fulfilled. The calibration procedure is based on firm scientific foundations so that it is easy to envision future improvements in accuracy and ease of implementation. Published 2007 Wiley-Liss, Inc. y Key terms multicolor cytometry; calibration; quantitation; biological standard IN a flow cytometer measurement, cells are carried by a flowing stream across focused laser beams (1). Prior to aspiration of the cells into the sheath fluid stream of the flow cytometer, the cells are incubated with a mixture of labeled antibodies specific to various receptors on the cell surface or intracellular protein antigens. Nuclear antigens can also be detected and are often useful as proliferation markers. After the incubation, the labeled antibodies are attached to specific receptors on the surface of the cell or intracellular protein antigens. As the cells flow past the laser beams, the fluorescence of fluorophores is detected in discreet fluorescence channels (FC) via photomultipler tubes (PMT). Fluorescence signal detected in a specific fluorescence channel is representative of the expression level of a given protein antigen. Because immune cells work in a cooperative manner (2), disease diagnostics and immunotherapies are mostly carried out by monitoring expression of multiple cell receptors, such as HIV-1 infection (3,4) and chronic lymphocytic leukemia (5,6). A CLSI guideline (7) exists for fluorescen...