Improved imaging of morphological changes has the potential of offering new insight into the complex process of embryonic development. Optical coherence tomography (OCT) is a new imaging technique for performing in vivo cross-sectional imaging of architectural morphology by measuring backscattered infrared light. This study investigates the application of OCT for imaging developing structure in Rana pipiens, Xenopus laevis, and Brachydanio rerio. Images are compared to conventional histological baselines. Cross-sectional imaging can be performed and structural morphology identified at greater imaging depths than possible with confocal and light microscopy. Repeated OCT imaging may be performed in vivo in order to track structural changes throughout development.