Scaphopods comprise about 900 described species of elongate infaunal molluscs, separated into two orders. The phylogenetic position of this class is contentious, having been proposed as a sister-group to bivalves or alternatively cephalopods, all groups that notably represent dramatic modifications of the molluscan body plan and historical confusion over the fundamental body axes. The digging scaphopod foot was previously considered to be anterior. Here we use a three-dimensional tomographic reconstruction of digestive anatomy and partial dorso-ventral musculature, to test the hypothesis that the scaphopod foot is ventral. Similar to cephalopods, the body orientation is confounded by ano-pedal flexion, but rationalising scaphopods is perhaps further undermined by their infaunal lifestyle, which confounds comparison of ecological life position. Some scaphopods are locally abundant, providing good quality material for anatomical study. In our focal species, Rhabdus rectius (Carpenter, 1864), sexes can reliably be differentiated in vivo by differential colour of the gonad (yellow in females; white in males). The gut is composed of three complete loops. Based on the orientation of the digestive tract and the dorso-ventral muscles, we find further evidence to support the interpretation that the concave side of the scaphopod shell is anterior (the site of the mouth) and the foot is ventral.