SummaryCardiovascular disease (CVD) involves the second cause of death in low‐risk myelodysplastic syndrome (MDS) population. Prospective study to characterise the CVD and to identify predictors for the combined event (CE) cardiovascular event and/or all‐cause mortality in transfusion dependent low‐risk MDS patients. Thirty‐one patients underwent a cardiac assessment including biomarkers and cardiac magnetic resonance (cMR) with parametric sequences (T1, T2 and T2* mapping) and myocardial deformation by feature tracking (FT) and were analysed for clonal hematopoiesis of indeterminate potential mutations. Cardiac assessment revealed high prevalence of unknown structural heart disease (51% cMR pathological findings). After 2·2 [0·44] years follow‐up, 35·5% of patients suffered the CE: 16% death, 29% cardiovascular event. At multivariate analysis elevated NT‐proBNP ≥ 486pg/ml (HR 96·7; 95%‐CI 1·135–8243; P = 0·044), reduced native T1 time < 983ms (HR 44·8; 95%‐CI 1·235–1623; P = 0·038) and higher left ventricular global longitudinal strain (LV‐GLS) (HR 0·4; 95%‐CI 0·196–0·973; P = 0·043) showed an independent prognostic value. These variables, together with the myocardial T2* time < 20ms, showed an additive prognostic value (Log Rank: 12·4; P = 0·001). In conclusion, low‐risk MDS patients frequently suffer CVD. NT‐proBNP value, native T1 relaxation time and longitudinal strain by FT are independent predictors of poor cardiovascular prognosis, thus, their determination would identify high‐risk patients who could benefit from a cardiac treatment and follow‐up.