In hypertrophic cardiomyopathy (HC), there are significant variations in left ventricular (LV) wall thickness and fibrosis, which necessitates a volumetric coverage. Slice-interleaved T₁ (STONE) mapping sequence allows for the assessment of native T₁ time with complete coverage of LV myocardium. The aims of this study were to evaluate spatial heterogeneity of native T₁ time in patients with HC. Twenty-nine patients with HC (55 ± 16 years) and 15 healthy adult control subjects (46 ± 19 years) were studied. Native T₁ mapping was performed using STONE sequence which enables acquisition of 5 slices in the short-axis plane within a 90 seconds free-breathing scan. We measured LV native T₁ time and maximum LV wall thickness in each 16 segments from 3 slices (basal, midventricular and apical slice). Late gadolinium enhanced (LGE) magnetic resonance imaging was acquired to assess the presence of myocardial enhancement. In patients with HC, LV native T₁ time was significantly elevated compared with healthy controls, regardless of the presence or absence of LGE (mean native T₁ time; LGE positive segments from HC, 1,141 ± 46 ms; LGE negative segments from HC, 1,114 ± 56 ms; segments from healthy controls, 1,065 ± 35 ms, p <0.001). Elevation of native T₁ time was defined as >1,135 ms, which was +2SD of native T₁ time by STONE sequence in healthy controls. A total of 120 of 405 (30%) LGE negative segments from patients with HC showed elevated native T₁ time. Prevalence of segments with elevated native T₁ time for basal, midventricular, and apical slice was 29%, 25%, 38%, respectively. Significant correlation was found between LV wall thickness and LV native T₁ time (y = 0.029 × −22.6, p <0.001 by Spearman's correlation coefficient). In conclusion, substantial number of segments without LGE showed elevation of native T₁ time, and whole-heart T₁ mapping revealed heterogeneity of myocardial native T₁ time in patients with HC.