There is rapid development in the field of protein microarray technology with the promise of important advancements in the near future. Protein microarrays have been reportedly successful in serum tumor marker profiling as well as in drug discovery and medicinal chemistry when the effect of small molecules in protein-protein interaction is studied. Some of the bottlenecks of the technology are protein instability, problems with immobilization and stabilization of proteins to the corresponding surface, as well as aspecific and /or not preferred interactions and the lack of protein amplification techniques to generate sufficient amounts of low abundance proteins. For the time being, the number of genes in RNA expression chips is significantly greater than the number of proteins available for microchip based analysis of gene expression at the protein level. The automation and standardization routinely used with nucleic acid microarrays is not yet available in their protein chip counterparts. One of the emerging applications of protein microchips is biomarker discovery via chromatographic surface-based protein array techniques, which is applicable to minute amounts of samples with excellent detection limits using mass spectrometry based interrogation. In this paper the advantages, technical limitations and main biomedical application of protein microarrays are reviewed.