Long bone shaft fragments can be found isolated in archaeological and forensic contexts, such as in mass fatality incidents. When diagnostic morphological landmarks are not visible, the assessment of a human or non-human origin of a bone fragment can be challenging. Further methods need to be developed. In long bones, the presence of a nutrient foramen on fragments that do not show any diagnostic landmarks can make the assessment of the origin of the bone still possible. In this paper, human long bones were compared to those of the following species: chicken (Gallus gallus domesticus), duck (Cairina moschata), sheep (Ovis aries), pig (Sus scrofa domesticus), and deer (fallow deer, Dama dama, and roe deer, Capreolus capreolus). Macroscopic evaluation of location, direction and appearance, and micro-CT scanning in order to measure angle and shape of canal entrance, were applied in this study to differentiate human from non-human nutrient foramina on long bone shafts. Observations regarding the location and direction of nutrient foramina were proven to be different between human and non-human bones; however, these two features might not be exploitable in cases of highly fragmented bones. The foramina appearance was the most reliable for the origin identification, although the shape of the canal entrance and its angle at the cortical bone, obtained