Extensive recent work has taken place on the construction of probabilistic atlases of anatomical organ. We propose a probabilistic atlas of ten major abdominal organs which retains structural variability by using a size-preserving affine registration, and normalizes the physical organ locations to an anatomical landmark. Restricting the degrees of freedom in the transformation, the bias from the reference data is minimized, in terms of organ shape, size and position. Additionally, we present a scheme for the study of anatomical variability within the abdomen, including the clusterization of the modes of variation. The analysis of deformation fields showed a strong correlation with anatomical landmarks and known mechanical deformations in the abdomen. The atlas and its dependencies represent a potentially important research tool for abdominal diagnosis, modeling and soft tissue interventions.