This paper presents a novel shape-guided multi-region variational region growing framework for extracting simultaneously thoracic and abdominal organs on 3D infants whole body MRI. Due to the inherent low quality of these data, classical segmentation methods tend to fail at the multi-segmentation task. To compensate for the low resolution and the lack of contrast and to enable the simultaneous segmentation of multiple organs, we introduce a segmentation framework on a graph of supervoxels that combines supervoxels intensity distribution weighted by gradient vector flow value and a shape prior per tissue. The intensity-based homogeneity criteria and the shape prior, encoded using Legendre moments, are added as energy terms in the functional to be op- timized. The intensity-based energy is computed using both local (voxel value) and global (neigboring regions mean values, adjacent voxels values and distance to the neighboring regions) criteria. Inter-region conflict resolution is handled using a weighted Voronoi decomposition method, the weights being determined using tissues densities. The energy terms of the global energy equation are weighted using an information on growth direction and on gradient vector flow value in order to either guide the segmentation toward the image natural edges if it is consistent with image and shape prior terms or enforce the shape prior term otherwise. Results on 3D infants MRI data are presented and compared to a set of manual segmentations. Both visual comparison and quantitative measurements show good results.