The diagnosis of cardiomyopathy states may benefit from machine-learning (ML) based approaches, particularly to distinguish those states with similar phenotypic characteristics. Three-dimensional myocardial deformation analysis (3D-MDA) has been validated to provide standardized descriptors of myocardial architecture and deformation, and may therefore offer appropriate features for the training of ML-based diagnostic tools. We aimed to assess the feasibility of automated disease diagnosis using a neural network trained using 3D-MDA to discriminate hypertrophic cardiomyopathy (HCM) from its mimic states: cardiac amyloidosis (CA), Anderson–Fabry disease (AFD), and hypertensive cardiomyopathy (HTNcm). 3D-MDA data from 163 patients (mean age 53.1 ± 14.8 years; 68 females) with left ventricular hypertrophy (LVH) of known etiology was provided. Source imaging data was from cardiac magnetic resonance (CMR). Clinical diagnoses were as follows: 85 HCM, 30 HTNcm, 30 AFD, and 18 CA. A fully-connected-layer feed-forward neural was trained to distinguish HCM vs. other mimic states. Diagnostic performance was compared to threshold-based assessments of volumetric and strain-based CMR markers, in addition to baseline clinical patient characteristics. Threshold-based measures provided modest performance, the greatest area under the curve (AUC) being 0.70. Global strain parameters exhibited reduced performance, with AUC under 0.64. A neural network trained exclusively from 3D-MDA data achieved an AUC of 0.94 (sensitivity 0.92, specificity 0.90) when performing the same task. This study demonstrates that ML-based diagnosis of cardiomyopathy states performed exclusively from 3D-MDA is feasible and can distinguish HCM from mimic disease states. These findings suggest strong potential for computer-assisted diagnosis in clinical practice.