This talk will cover the basics of optical coherence tomography (OCT), and ongoing applications of OCT in my lab. OCT is a standard-of-care imaging technique for the eye. It provides microscopic resolution at deeper imaging depths than microscopy, is low-cost, and does not require contact with the sample. However, traditional OCT is not sensitive to molecular sources of contrast. We have developed a molecular OCT technique, photothermal OCT (PT-OCT) that is sensitive to endogenous and exogenous contrast agents. PT-OCT uses the photothermal effect to locate light absorbers in a sample, which change the optical path length in the local region. PT-OCT has been used to image melanin and gold nanorod contrast agents in vivo in a mouse model of eye neovascularization. This technology could provide new sources of contrast to understand and combat eye diseases. We have also used OCT to monitor cilia-driven fluid flow in ex vivo trachea, to relate cilia function and metabolism measured with auto-fluorescence microscopy. Finally, OCT angiography has been used to image 3D microvascular morphology in vivo in the mouse, to monitor the effect of pro-angiogenic therapies for peripheral artery disease.