Optical coherence tomography (OCT) is a new method of biomedical imaging that can generate high-resolution, cross-sectional images of microstructures. The purpose of this study was to present the first OCT images of oral vascular anomalies using a new advanced OCT scanner that we have developed, and to discuss the application of our system for oral soft tissues. Knowledge of the size and area of the vascular structures can be useful for the diagnosis and choice of the best treatment. Before excision, oral vascular malformations were assessed by OCT in vivo. Histopathological sections were taken and compared with the OCT images to make clinicopathological correlations. OCT provided clear images of all the vascular lesions examined. Oval to roundish, signal-poor areas sharply demarcated by a surrounding signal-rich layer correlated well with the histopathological diagnosis. OCT images provide information about subsurface structure non-invasively that is otherwise obtainable only by examination of a biopsy specimen. The analysis of oral vascular lesions by OCT provides new insights into non-invasive diagnosis and can be helpful in the selection of the most appropriate treatment.