The success of genome sequencing projects has led to a shift from the description of single molecules to the characterisation of complex samples. At the same time, there is growing interest not only in studying organisms at the genomic level, but in the characterization of their proteome. Such a task would not be possible without the availability of appropriate technologies. Protein and antibody microarray technologies are, in addition to two-dimensional gel electrophoresis followed by mass spectrometry, two of the most propitious technologies for the screening of complex protein samples. Nevertheless, to succeed, protein and antibody microarrays have to overcome their current limitations. This review aims to introduce these new technologies and highlights their current prospects and limitations.