Fluorescence microscopy is an important and fundamental tool for biomedical research. Optical microscopy is almost non-invasive and allows highly spatially resolved images of organisms, cells, macromolecular complexes, and biomolecules to be obtained. Generally speaking, the architecture of the observed structures is not significantly modified and the environmental conditions can be kept very close to physiological reality. The development of fluorescence microscopy was revolutionized with the invention of laser scanning confocal microscopy (LSCM). With its unique three-dimensional representation and analysis capabilities, this technology gives us a more real view of the world. This chapter introduces the reader to the methodology of setting up basic experiments for use with a laser scanning confocal microscope. There are practical guidelines about sample preparation for both fixed and living specimens, as well as examples of some of the applications of confocal microscopy.