Two-photon microscopy is an especially powerful tool for combining anatomical and physiological experiments in the central nervous system: the possibility of simultaneously studying physiological phenomena in well-defined anatomical compartments allows fluorescence imaging of neurons in deeper layers of the brain. In this review we summarize the most commonly used brain preparation techniques together with the methods of loading neurons with fluorescent indicators. We will focus primarily on issues of drug delivery specifically related to two-photon experiments highlighting the different ways of drug administration. Methods of chemical stimulation via caged neurotransmitters are also discussed. Finally a few specific areas of two-photon applications in drug research on neuronal tissue are highlighted.