AbstractPair‐matching of bilateral elements is a major component of resolving commingled remains both in forensic and bioarchaeological contexts. This study presents a new method of osteometric pair‐matching of the lower limbs which relies on 3D digital models of the femur and tibia bones. The proposed method, which is accompanied by a freely available open‐source implementation, automatically computes a number of osteometric variables including cross‐sectional geometric properties from an assemblage of left and right bone antimeres and calculates probabilistically the appropriate matching pairs as well as single elements, whose bones antimere is not present in the given assemblage. The method has been extensively tested on a skeletal sample comprising 396 femurs and 422 tibias from the Athens collection. Our results in testing commingled assemblages with no disparity show that the method’s sensitivity is 1 for sorting femurs and 0.997 for sorting tibias, whereas in assemblages with moderate disparity the sensitivity is 0.999 and 0.992 respectively. Our results further indicate that sensitivity is unaffected by the size of the commingled assemblage although the percentage of identified true matching pairs drops as the number of commingled elements increases. This means that all identified antimeres matched to an individual are still very accurately sorted despite not every individual being identified in very large assemblages. The proposed method can facilitate the sorting process of commingled remains both accurately and efficiently, while leaving a very small percentage of unsorted elements that may require further techniques for further individualization.