NeuroQuant (NQ) is a fully-automated program that overcomes several existing limitations in the clinical translation of MRI-derived volumetry. The current study characterized differences between the original (NQ1) and an updated NQ version (NQ2) by (i) replicating previously identified relationships between neuropsychological test performance and medial temporal lobe volumes, (ii) evaluating the level of agreement between NQ versions, and (iii) determining if the addition of NQ2 age-/sex-based z-scores hold greater clinical utility for prediction of memory impairment than standard percent of intracranial volume (%ICV) values. Sixty-seven healthy older adults and 65 MCI patients underwent structural MRI and completed cognitive testing, including the Immediate and Delayed Memory indices from the RBANS. Results generally replicated previous relationships between key medial temporal lobe regions and memory test performance, though comparison of NQ regions revealed statistically different values that were biased toward one version or the other depending on the region. NQ2 hippocampal z-scores explained additional variance in memory performance relative to %ICV values. Findings indicate that NQ1/2 medial temporal lobe volumes, especially age- and sex-based z-scores, hold clinical value, though caution is warranted when directly comparing volumes across NQ versions.