Background. We assessed the usefulness of a longitudinal strain adjusted to regional thickness in hypertrophic cardiomyopathy (HCM). Indeed, with conventional software, the width of the region of interest (ROI) is the same over the entire myocardial wall, wherein the software analyzes only partially the left ventricular (LV) hypertrophic segments. Methods. We included 110 patients: 55 patients with HCM (HCM group) and 55 healthy subjects (age-and sex-matched control group). The global longitudinal strain (GLS) and regional strain for each of the 17 segments was calculated with standard software (for two groups) and with software adjusted to the myocardial wall thickness (for the HCM group). Results. GLS was significantly decreased in the HCM group compared to the control group (−15.1 ± 4.8% versus −20.5 ± 4.3%, p < 0.0001). In the HCM group, GLS (standard method versus adjusted to thickness) measurements were not significantly different (p = 0.34). Interestingly, the regional strain adjusted to thickness was significantly lower than the standard strain in the hypertrophic segments, especially in the basal inferoseptal segment (p = 0.0002), median inferoseptal segment (p < 0.001) and median anteroseptal segment (p = 0.02). The strain adjusted to thickness was still significantly lower in the most hypertrophic segments (≥20 mm) (−3.7 ± 3%, versus −5.9 ± 4.4%, p = 0.049 in the basal inferoseptal segment and −5.7 ± 3.5% versus −8.3 ± 4.5%, p = 0.0007 in the median inferoseptal segment). In the segments with significant myocardial fibrosis, the longitudinal strain adjusted to thickness was significantly lower than the conventional strain (−8.3 ± 3.3% versus −11.4 ± 4.5%, p = 0.002). The analysis of the strain adjusted to thickness had a better feasibility (97.5% versus 99%, p = 0.01). Conclusions. The analysis of a longitudinal strain adjusted to regional thickness is feasible in HCM and allows a better evaluation of myocardial deformation, especially in the most LV hypertrophic segments.