Microarray technology plays an increasing role in proteomic research. We give an overview about recent developments in this technology focusing on molecular interaction studies using protein and antibody microarrays. We report about technical aspects in the development of protein microarrays and describe different surfaces and detection modes. Furthermore, we review the applications of protein microarrays in different molecular interaction studies including interactions of proteins with antibodies, proteins, DNA, small molecules and enzymes. Advantages and limitations of the microarray-based methods with other in vitro methods have been compared. We present the increasing applications of protein and antibody microarrays in basic research, diagnostics, drug discovery, and in vitro-risk assessment of nutrients.