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. The 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.