Microscopy is traditionally a tool for determining biological structures. Many recent advances in optical microscopy involves the incorporation of spectroscopy techniques to monitor biochemical states of microscopic structures in living cells and tissues. By minimizing tissue photodamage, two-photon excitation microscopy provides a new opportunity to study the dynamics of biological systems on time scales from nanoseconds to hours. This review will focus on a number of these new methods: two-photon time-lapse microscopy, two-photon photoactivation, two-photon correlated spectroscopy, two-photon single particle tracking and two-photon lifetime microscopy.