Over the past decade, two-photon microscopy has successfully made the transition from the laser laboratory into a true biological research setting. This has been due in part to the recent development of turnkey ultrafast laser systems required for two-photon microscopy, allowing ease of use in nonspecialist laboratories. The advantages of two-photon microscopy over conventional optical sectioning techniques are for greater imaging depths and reduced overall phototoxicity, as such enabling noninvasive intra-vital imaging of cellular and subcellular processes. Greater understanding of these advantages has allowed this technique to be more effectively utilized in a biological research setting. This review will cover the recent widespread uses of two-photon microscopy and highlight the wide range of physiological studies enabled in fields such as neurosciences, developmental biology, immunology, cancer biology, and endocrinology.