Tissue microarrays (TMAs) are composite tissue blocks capable of accommodating over 1,000 unique tissue cores on a single glass slide. TMAs have become widely adopted in pathology and biomarker research. This chapter briefly discusses the design and construction of TMAs, the state of TMA imaging, and current methods for the analysis and management of TMA data. A significant portion of the chapter highlights the technical challenges of using formalin-fixed, paraffin embedded tissue and analyzing tissue stained using immunohistochemistry (IHC).