Cytokines, which are small peptides that act as hormones of the immune system, affect cells throughout the body in a variety of different ways. These cellular signaling molecules often have synergistic or opposing effects on various cell types and often different cytokines have overlapping activities. There is great advantage, therefore, to be able to assess a pattern of cytokine responses in certain inflammatory, autoimmune, transplant or immunodeficiency states. This is one of the major advantages of the new particle-based flow cytometric assays, which have become available. We have employed such assays to analyze up to 10 different cytokines in cultured supernatants of stimulated mononuclear cells and in as little as 75 microL of serum from patients with a variety of different disorders. In developing these assays and validating them for use in our esoteric reference laboratory (ARUP Laboratories), we have found that a variety of heterophile antibodies can lead to both false positive and false negative results. This review will describe the development of our multi-analyte cytokine assays and document the interference derived from heterophile antibodies. Lastly, we will point out various procedures that we have utilized to include internal controls directly in the assays, which allow one to routinely detect these interfering antibodies, as well as methods we have developed to circumvent the interference posed by these antibodies.