This study examines quantification techniques applicable to human skeletal remains, and in particular the Lincoln index (LI), the minimum number of individuals (MNI), and what we refer to as the most likely number of individuals (MLNI), which is a modification of the LI by Chapman ( Univ. Calif. Publ. Stat. 1:131–159). As part of the study, a test of pair-matching between commingled homologous elements, e.g., right and left femora, was performed based on gross morphology. The results show that pair-matching can be accurately performed, and that the MLNI is a useful technique for dealing with well-preserved commingled remains recovered from archaeological excavations and/or forensic investigations. Our results show that it is potentially misleading to draw population conclusions based on the MNI, except in instances where recovery is near 100%. The MLNI was found to be the best method to compensate for the potential underestimates of the MNI and potential bias in the original LI estimates resulting from small sample sizes. We demonstrate the use of MLNI in estimating the number of individuals from Lodge 21 at the Larson site, a late protohistoric structure at which the inhabitants were massacred and subsequently had their skeletal elements commingled by further taphonomic processes. We also show how to calculate estimates and standard errors for the recovery probabilities of skeletal elements. Am J Phys Anthropol, 2004. © 2004 Wiley-Liss, Inc.