Background: The cardiac Magnetic Resonance Imaging (MRI) characteristics of rare diseases with the hypertrophic cardiomyopathy (HCM) phenotype are not well defined. Methods: Seventy-three sequential patients and 34 of their relatives, who have the HCM phenotype, were included. All subjects underwent cardiac MRI and genetic testing. Results: Of these 107 patients with phenotypic HCM, seven rare diseases were identified: four cases with LAMP2, one case with PRKAG2, one case with TTR mutation, and one case with senile systemic amyloidosis. Subjects with rare diseases had diffuse LGE, and the percentage of those with LGE was significantly higher than that of other HCM (median: 18.9%, interquartile range (IQR): 14.05 to 28.2% versus 7.8%, IQR: 4.41 to 14.56%; p = 0.003). Additionally, global T1 and ECV were significantly higher in subjects with rare diseases (global T1: 1423.1 ± 93.3 ms versus 1296.2 ± 66.6 ms; global ECV: 44.3 ± 11.5% versus 29.9 ± 4.5%; all p < 0.001). Conclusions: Cardiac MRI suggests the existence of distinct imaging characteristics, including via LGE and T1 mapping, among rare diseases that mimic HCM and HCM itself.