Microarray technologies are state of the art in biological research, which requires fast genome, proteome and transcriptome analysis technologies. Often antibodies are applied in protein microarrays as proteomic tools. Since the generation of antibodies against toxic targets or small molecules including organic compounds remains challenging the use of antibodies may be limited in this context. In contrast to this, aptamer microarrays provide alternative techniques to circumvent these limitations. In this article we review the latest developments in aptamer microarray technology. We discuss similarities and differences between DNA and aptamer microarrays and shed light on the post synthesis immobilization of aptamers including corresponding effects on the microarray performance. Finally, we highlight current limitations and future prospects of aptamer microarray technology.