Immunohistochemistry (IHC) is the gold standard methodology for in-situ protein expression analysis in tissue samples. The combination of IHC and tissue microarray (TMA) technology allows for the simultaneous analysis of hundreds of tissue samples with an unprecedented degree of experimental standardization. The same immunostaining protocols used for conventional large sections can be used for TMAs, including antigen retrieval procedures for staining of routinely archived formalin-fixed tissue samples. The development of optimal IHC protocols is highly important for TMA studies because minor protocol variations often have a marked impact on the outcome of the staining. Preabsorption and isotype-specific control experiments should be included as the last step in protocol development to proof target protein-specific binding. Such controls are particularly important for new antibodies with unknown staining patterns.