The aim of the study was to evaluate the presence and spectrum of cardiac abnormalities identified by cardiac magnetic resonance (CMR) in subjects in clinical remission of Churg-Strauss syndrome (CSS) and granulomatosis with polyangiitis (Wegener's) (WG) with normal ECG and transthoracic echocardiography (TTE). Eleven (7 females, 4 males, mean age 42.4 ± 9.6 years) CSS and 10 (4 females, 6 males, mean age 45.3 ± 10.9 years) WG patients in clinical remission with normal ECG and TTE underwent CMR. Segmental peak-systolic myocardial strain (εps) was measured using feature tracking cine-sequence based technique. Left ventricular (LV) ejection fraction, end-diastolic volume and myocardial mass indexes were 66.2 ± 5.8 %, 66.1 ± 6.6 ml/m(2), and 61.0 ± 8.9 g/m(2), respectively. No patient showed regional wall motion abnormalities and signs of myocarditis. Nine CSS and 8 WG patients demonstrated decreased segmental longitudinal, circumferential or radial εps and myocardial late gadolinium enhancement (LGE) (6 subendocardial, 10 midwall, 8 subepicardial) areas. In CSS and WG subjects with LVLGE lesions the mean LVLGE extent was 2.0 ± 1.6 % and 2.3 ± 1.5 % (p = 0.65), respectively. Segmental εps was decreased longitudinally (-11.8 ± 5.6 %) for subendocardial LGE, radially (13.7 ± 8.7 %) for subepicardial LGE, and circumferentially (-16.6 ± 4.2 %), longitudinally (-13.2 ± 5.5 %) and radially (18.8 ± 8.1 %) for midwall LGE, if compared to longitudinal (-22.7 ± 5.1 %), circumferential (-23.6 ± 5.6 %) and radial (34.2 ± 15.7 %) εps in controls (11 females, 10 males, mean age 43.9 ± 10.5 years) (all p < 0.01). Despite clinical remission, normal ECG and TTE, most CSS and WG patients demonstrate decreased segmental εps and non-ischemic LGE lesions without signs of myocarditis.