One of the great hopes in biomedical research is that proteomic technology can be used to identify novel biomarkers for diseases such as cancer. The challenge to discovering biomarkers starts with sample collection and continues right through data acquisition and bioinformatic analysis. Because the ultimate goal is to find indicators of human disease it is ideal to be able to study clinical samples. Unfortunately clinical samples such as serum, plasma, urine, and especially tissue biopsies are precious and are often difficult to obtain in sufficient quantities or numbers to conduct proteomic discovery studies. There exists, however, a vast archive of pathologically characterized clinical samples in the form of formalin fixed paraffin embedded tissue blocks. This chapter describes methods that have been developed to allow the proteins from these tissue samples to be excised in a form that is amenable for proteomic analysis by mass spectrometry.