Left ventricular hypertrophy (LVH) is a complex cardiac condition mainly identified by the thickening of the myocardial wall. Although most of the contemporary cardiac imaging modalities provide high resolution 3D images, the wall thickness (WT) is still measured within the acquired planes. This way of measurement may introduce an error as cardiac wall is not necessarily orthogonal to the plane. In this study we analyze how different approaches to measure WT can affect an automatic identification of hypertrophy. The compared approaches are: WT measured along surface normal and the one provided by a medial surface. For both approaches we evaluated their ability to identify LVH phenotypes by testing with two classifiers: Transductive Confidence Machine-k Nearest Neighbor (TCM-kNN) and Linear Discriminant Analysis (LDA). Fifty three subjects were included in this study: 18 patients with hypertrophic cardiomyopathy (HCM), 13 patients with hypertensive heart disease (HDD) and 22 sedentary subjects (CG). Medial surface based approach allowed obtaining higher classification accuracy in HDD patients, while normal based approach allowed for higher classification accuracy in HCM patients.