Three-dimensional (3D) speckle tracking echocardiography (STE) is a reliable clinical tool for accurate measurements of left ventricular (LV) volumes and ejection fraction (EF). In this prospective study, we sought to identify an association between 3DSTE longitudinal strain abnormalities and areas of late gadolinium enhancement (LGE). In 50 patients (52 ± 18.5 years old) referred to our hospital for clinically indicated CMR, 3D full-volume trans-thoracic acquisitions on apical views were performed within 1 h of CMR, in order to obtain LV volumes and ejection fraction as well as global and segmental peak systolic longitudinal strain. Relative amount of fibrosis was defined based on LGE CMR with grey-scale threshold of 5 standard deviations above the mean signal intensity of the normal remote myocardium. We found a moderate positive correlation between global longitudinal strain (GLS) by 3DSTE and LGE proportion (r = 0.465, p = 0.001). The area under the receiver operating characteristic curve was 0.79. In addition, abnormal GLS could detect LGE-determined myocardial fibrosis with a sensitivity of 84.6%, a specificity of 84.8%, a positive predictive value of 69% and negative predictive value of 93%, considering an optimal GLS cut-off value of − 15.25%. Regarding 3DSTE capacity of localizing segmental LGE involvement, about 70% of LGE-positive segments presented a concomitant longitudinal strain reduction. This prospective study shows that 3DSTE longitudinal deformation is moderately associated with the extent of myocardial fibrosis, with a promising potential role in ruling out prognostically relevant fibrosis as detected by LGE.