: Medial temporal lobe atrophy (MTA) remains an important imaging biomarker in brain magnetic resonance imaging (MRI) for diagnosing and evaluating Alzheimer's disease (AD). We compared the detection performance for determining significant MTA and the correlation with Scheltens' scale between two automatic volumetry software, NeuroQuant® and Aqua®, in non-AD and AD groups. Overall, 127 (non-AD, 54; AD, 73) individuals who underwent three-dimensional T1-weighted volumetric MRI in our hospital between January and August 2011 were enrolled and retrospectively analyzed using NeuroQuant® and Aqua®. The accuracy, sensitivity, and specificity for detecting significant MTA and the correlation for Scheltens' scale with the mean hippocampal volume of each software were evaluated. The study sample’s mean age was 78 (range, 59–97) years. Regarding accuracy and specificity, Aqua® was non-inferior to NeuroQuant®. Aqua® had significantly higher overall specificity than NeuroQuant® for detecting significant MTA. Additionally, the calculated mean hippocampal volume of Aqua® was more correlated with Scheltens' scale (Kendall's τ, - 0.48) than that of NeuroQuant® (Kendall's τ, - 0.20). The accuracy and specificity of Aqua® in detecting MTA are not inferior to those of NeuroQuant®. Additionally, Aqua® has a stronger correlation of mean hippocampal volume with Scheltens' scale than NeuroQuant®.