The mouse is the most appropriate biomedical model organism for researching the mechanistic function of genetic factors in normal embryogenesis and in the genesis of cardiovascular malformations. Three-dimensional (3D) visualisation of the developing organs of wild type and genetically modified mouse embryos is essential for such research. This paper aims at discussing imaging methods that permit the generation of digital volume data sets, which fit for the virtual 3D visualisation and 3D analysis of the cardiovascular system of mouse embryos and mouse fetus. To cover the spectrum of imaging methods comprehensively, we will start with a short overview about early 3D-reconstruction techniques. This will be followed by a brief discussion why in vivo imaging techniques, such as ultrasound (US) or optical coherence tomography (OCT) do not fit for constructing volume data sets that permit virtual 3D visualisation of the cardiovascular system of mouse embryos/fetus. We will then briefly introduce techniques, which permit 3D analysis of the cardiovascular system but do not fit for creating digital volume data (corrosion casts, scanning electron microscopy). Finally, we will focus on describing the advantages and disadvantages, the spectrum of application and the limitations of important modern digital volume data generation methods, such as micro-computed tomography (µCT), micro-magnetic resonance imaging (µMRI), optical projection tomography (OPT), confocal microscopy, histological section based volume data generation methods, and 3D episcopic imaging methods.