Affymetrix Inc. developed a novel assay for the simultaneous detection of mRNA and its corresponding proteins. The technique of the Prime RNAFlow™ assay is based on the labeling of proteins by fluorescent antibodies, as well as the detection of mRNA molecules by hybridization with fluorescence labeled probes. First, surface staining is done, after the fixation and permeabilization of the cells intracellular proteins can be labeled. This is followed by a multi-stage hybridization protocol with gene-specific probes, pre-amplifiers, amplifiers and fluorescence labeled probes. In this assay, there are three types of labels, type 1, type 4 and type 6, which can supposedly be used in a multiplex method. Each of these labels consists of different pre-amplifiers, amplifiers and fluorescence labeled probes. The type 1 label with the fluorescent dye Alexa Fluor 647 is applied for the detection of low and unknown expression levels. On the other hand, for the detection of medium to high levels of expression the type 4 labeling with Alexa Fluor 488 and the type 6 labeling with Alexa Fluor 750 can be used. In my work I have tested the general functionality of the assay and the three different labels by expression analysis of actin-β, CD4 and interferon-γ in differentially stimulated cells. My results show that the simultaneous detection of mRNA and proteins is possible, but is subject to certain limitations. Only the type 1 label provided plausible results, since with both the type 4 as well as the type 6 label hardly any signals could be measured. Furthermore, it appears that a possible cross-reactivity between the types of labels could be present.