The purpose of this study was to use multidimensional scaling (MDS) and cluster-analytic techniques to examine how cytokine levels from a large multiplex assay of human milk samples covary. Milk samples were collected at 4-6 weeks postpartum from 57 women and were assayed by Luminex multiplex technology for 20 cytokines, chemokines, and growth factors. The MDS was applied to a proximity-score matrix based on these values. A three-dimensional (3D) space was sufficient to accommodate the configuration of relationships. Cytokines that covaried in their concentrations were assigned similar coordinates and plotted close together in 3D space. Several clusters of cytokines were identified. Since very little is known about the origins and functions of cytokines in milk, this approach may provide new clues that will guide future explorations of origins and functional relationships of the separate clusters. This analytical tool may provide a new approach to understanding the physiology of milk cytokines and may be generalizable to multiplex data in general.