Highly multiplexed assays using antibody coated, fluorescent (xMap) beads are widely used to measure quantities of soluble analytes, such as cytokines and antibodies in clinical and other studies. Current analyses of these assays use methods based on standard curves that have limitations in detecting low or high abundance analytes. Here we describe SAxCyB (Significance Analysis of xMap Cytokine Beads), a method that uses fluorescence measurements of individual beads to find significant differences between experimental conditions. We show that SAxCyB outperforms conventional analysis schemes in both sensitivity (low fluorescence) and robustness (high variability) and has enabled us to find many new differentially expressed cytokines in published studies.