Gene profiling and expression analysis using microarrays have made a significant impact on our biological understanding of prostate cancer. The procedures for generating high-quality expression data from prostate cancer cell lines and tumors are not trivial. However, during the past 9 years, methods by which to process samples for gene profiling have been developed. In this chapter, techniques to process prostate cancer specimens either en bloc (macrodissection) or using laser capture microdissection are presented in detail along with extensive technical notes. Although we focus on prostate cancer and discuss the specific methods utilized in our lab, the processes discussed are generalizable to other tumors and amenable to the substitution of alternative instruments and/or commercially available kits.