Background Hypertrophic cardiomyopathy (HCM) is one of the commonest inheritable cardiac disorders. Being a global disease with diffuse myocardial fibrosis, it has a wide range of adverse outcomes ending with sudden cardiac death. Cardiac magnetic resonance (CMR) with late gadolinium enhancement (LGE) has become a reference standard for visualization of focal myocardial fibrosis. In the setting of less severe or more diffuse fibrosis, LGE is unlikely to reveal the presence of abnormal tissue given the lack of normal myocardium as a reference. Direct measurement of myocardial T1 time (T1 mapping) may improve these methodologic problems of LGE CMR in the setting of diffuse retention of gadolinium-based contrast material. So, we aim at this study to evaluate the clinical application of CMRI native and post-contrast T1 relaxation in assessing diffuse myocardial fibrosis non-invasively in hypertrophic cardiomyopathy. Results There was a significant difference between the percent of fibrosis detected by measuring the extracellular volume percent compared to that detected by LGE, with the former detecting fibrosis in 45.1% of the examined cardiac segments while the latter showed fibrosis in 20.9% of the cardiac segments. Also, measuring the native T1 values showed evidence of fibrosis in about 32.2% of the cardiac segments superseding the percent of fibrosis detected using the LGE alone. The ejection fraction percent showed a negative correlation with the left ventricular mass with a correlation coefficient value of − 0.139 where both interstitial and replacement fibrosis play an important role in the pathophysiology of diastolic dysfunction as well as impairing the myocardial contractility. Also, in cases of obstruction, the extracellular volume (ECV) is more likely to increase in the basal anterior and antero-septal segments as well as the basal inferior segment with P values 0.015, 0.013, and 0.045, respectively. Conclusion Diffuse fibrosis was found to be difficult to be distinguished using LGE. The unique ability of CMR to use proton relaxation times provides a quantitative measurement to detect increased interstitial volume in diffuse myocardial fibrosis. Moreover, it showed that in cases of obstruction, the segments exposed to the highest pressure are more vulnerable to the fibrotic process denoting a relationship between the pressure gradient and the adverse myocardial remodeling.