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A high incidence of isolated left ventricular non-compaction (LVNC) has been reported in previous studies on smaller cohorts of patients with thalassemia by cardiac MRI but the clinical impact of the finding is unknown. This prospective cohort study evaluates the prevalence and clinical implication of the finding. Prospective cohort study with enrollment of all consecutive cases with thalassemia referred for cardiac MRI from September 2007 to November 2014. The presence of LVNC was assessed according to the Petersen method and the Jacquier method, with the proposed changes by Fazio, Grothoff, and Chiodi. A clinical follow-up was performed in all patients. We included 560 patients with thalassemia (473 with thalassemia major and 87 with thalassemia intermedia: mean age 31.9 ± 10.6 years, male/female = 250/310). A total number of 1683 MRI tests were performed. A diagnosis of LVNC was determined according to adopted MR criteria in 44 patients (7.9%). Patients with LVNC had a significantly lower ejection fraction (52.68 ± 5.17% vs. 56.90 ± 6.34%; p = 0.0005) and greater indexed LV ESV (48.16 ± 10.03 ml/m 2 vs. 40.02 ± 10.06 ml/m 2 ; p = 0.0022). After a mean follow-up time was 5.1 years, no significant change of MR parameters was detected as well as no clinical adverse events. LVNC is relatively frequent in patients with thalassemia. However, it is not associated with a worsening of LV function and adverse events after a long-term follow-up.