Innovations in molecular medicine provided sophisticated tools for analysis of the pathogenesis of diseases. Much emphasis is put on examination of alterations in affected organ systems. However, since in vivo tissues are inherently complex mixtures of different cell types, specific molecular data on individual cell populations are difficult to obtain. The advent of laser assisted microdissection (LAM) now allows efficient isolation of pure cell populations and even of single cells from mixed tissues. The most promising aspect of LAM is its combination with different molecular downstream analyses of microdissected cells at the levels of the genome, the transcriptome and the proteome. This review focuses on the two basic techniques of laser-assisted microdissection and on its applications in molecular pathology.