Conventional microscopic techniques, to study embryonic development, require large numbers of embryos and are invasive, making follow-up impossible. We explored the use of in vivo MRI to study embryonic development, in general, and cardiovascular development in particular, over time. Wild-type quail embryos (n = 11) were imaged at embryonic days 3, 5, 7, 9, and 11, covering the main time course of embryonic heart development. On each imaging day cardiac morphology was evaluated and embryonic length was measured. MRI-embryos as well as control embryos (n = 11) were sacrificed at day 11 and scored for external malformations, while embryonic wet weight and stage were determined. In addition, venous clipped embryos (n = 4), known to develop cardiovascular malformations, were scanned at regular intervals and sacrificed at day 9 for histological analysis ex vivo. We were able to follow heart development of individual quail embryos inside their shell non-invasively over time, with sufficient detail to study cardiac morphology in vivo. We did not find any adverse effect of the repeated MRI examinations on morphology, length, or weight. Prenatally diagnosed malformations, like ventricular septal defects and aortic arch interruptions were confirmed by histology. In conclusion, micro-MRI can be used to evaluate in vivo early embryonic development and to diagnose cardiovascular malformations prenatally.