The mouse model is widely used to assess the origin of congenital heart malformations because of similarities between the mouse and human heart. However, the small size of the mouse heart challenges the use of human imaging techniques. Here, we propose a novel imaging pipeline in the mouse to characterize congenital heart malformations and their potential association with situs malposition. Using Micro Computed Tomography, the position and asymmetric shape of internal organs can be extracted. We propose a list of anatomical differences between mouse and human internal organs (e.g.: common ostium of pulmonary veins). To gain higher resolution in the diagnosis of heart malformations we then use High Resolution Episcopic Microscopy on explanted hearts, which can resolve the left/right morphology of atria and ventricles (Fig. 1). Alongside this high-resolution pipeline in fixed samples, we also use live imaging of embryonic hearts in utero, by echography, to correlate in the same heart, the embryonic shape with congenital heart malformations at birth. This strategy will be generally useful to analyze mouse mutants and provide novel insight into the mechanism of congenital heart defects.