The inertial properties of body segments reflect performance and locomotor habits in primates. While Pan paniscus is generally described as more gracile, lighter in body mass, and as having relatively longer and heavier hindlimbs than Pan troglodytes, both species exhibit very similar patterns of (quadrupedal and bipedal) kinematics, but show slightly different locomotor repertoires. We used a geometric model to estimate the inertial properties for all body segments (i.e. head, trunk, upper and lower arms, hand, thigh, shank and foot) using external length and diameter measurements of 12 anaesthetized bonobos (eight adults and four immatures). We also calculated whole limb inertial properties. When we compared absolute and relative segment morphometric and inertial variables between bonobos and chimpanzees, we found that adult bonobos are significantly lighter than adult chimpanzees. The bonobo is also shorter in head length, upper and lower arm lengths, and foot length, and is generally lighter in most absolute segment mass values (except head and hand). In contrast, the bonobo has a longer trunk. When scaled relative to body mass, most differences disappear between the two species. Only the longer trunk and the shorter head of the bonobo remain apparent, as well as the lighter thigh compared with the chimpanzee. We found similar values of natural pendular periods of the limbs in both species, despite differences in absolute limb lengths, masses, mass centres (for the hindlimb) and moments of inertia. While our data contradict the commonly accepted view that bonobos have relatively longer and heavier hindlimbs than chimpanzees, they are consistent with the observed similarities in the quadrupedal and bipedal kinematics between these species. The morphological differences between both species are more subtle than those previously described from postcranial osteological materials.