The medical history and clinical presentation associated with deep infantile hemangiomas (DIHs) and early venous malformations (EVMs) can be much confusing. The purpose of this study was to evaluate the role of 3D computed tomography angiography (3D-CTA) in differential diagnosis of DIHs and EVMs. A total of 18 infants with subcutaneous vascular lesions were included in this study. They were evaluated by CTA with 3D reformations of maximum intensity projection (MIP) and volume rendering. Appearance and vascularization of the lesions were analyzed. In this study, 3D-CTA findings were compared with the final diagnoses established by pathology. The final diagnoses included 11 DIHs and 7 EVMs. The 3D-CTA images accurately diagnosed DIH and EVM in all cases. In both MIP and volume rendering images, DIH showed an unique appearance of a compact solid mass with feeding vessels. While EVM demonstrated an ill-defined area with a tangle of vessels rather than a solid mass. Their distinct 3D-CTA features are helpful for differential diagnosis.