We present a review of imaging deep-tissue structures with multiphoton microscopy. We examine the effects of light scattering and absorption due to the optical properties of biological sample and identify 1300 nm and 1700 nm as ideal excitation wavelengths. We summarize the availability of fluorophores for multiphoton microscopy as well as ultrafast laser sources to excite available fluorophores. Lastly, we discuss the applications of multiphoton microscopy for neuroscience.