Within recent years, protein microarrays have beendeveloped to quantify a large number of parameters present ina given sample simultaneously. Such miniaturised andparallelised sandwich immunoassays are of general interest forall proteomic and diagnostic approaches in which severalparameters have to be determined from small samples, e.g.biopsy material. In addition to planar microarray-basedapproaches, bead-based flow cytometry is quite suitable for themultiplex detection of target molecules, especially when alimited number of parameters are to be analysed. Appropriatesensitivity, reproducibility and robustness have to bedemonstrated before protein microarray technology can beused to characterise clinical samples and generate reliable datasets. As a model system to analyse these issues, a set ofmultiplexed sandwich immunoassays based on Luminex beadswere developed to screen clinical samples for the presence orabsence of marker proteins indicative of prognosis or responseto therapeutic options.