The determination of the number of individuals represented within commingled remains is based on two types of estimators, those assessing the minimum number of individuals and those assessing the most likely number of individuals. Much as the latter produce improved results, they still exhibit significant drawbacks, which are related to the misidentification of the number of pairs between the existing bilateral elements. This article addresses these problems through the use of two computer algorithms. One algorithm produces a number of potential pairs between bilateral elements and the other estimates the number of individuals in a commingled sample by incorporating the percentages of lost and altered bones into the analysis. These algorithms were validated using hypothetical and actual skeletal samples, and are more effective in comparison to any conventional estimators, particularly in cases, where the elements are poorly preserved.