Expert laboratorians noted for their optimized methods describe in step-by-step detail how to successfully carry out tissue-based laser microdissection in their own laboratory using the different systems available and to apply a wide range of sophisticated molecular technologies to the microdissected tissue samples. Highlights include gene expression profiling of primary tumor cell populations using laser capture microdissection, RNA transcript amplification and GeneChip® microarrays, laser capture microdissection and colorectal cancer proteomics, and proteomic analysis of human bladder tissue using SELDI® approach following microdissection techniques. Applications of the microdissected tissue described encompass PCR, gene expression studies including microarray analysis, and proteomics.