The aim is to detect early changes in myocardial mechanics in hypertrophic cardiomyopathy (HCM) mutation carriers, three-dimensional speckle tracking echocardiography (3DSTE) was used for screening of family members in the HCM population. Eighty subjects were divided as: HCM mutation carriers (n = 23), manifest HCM patients (n = 28), and normal controls (n = 29). They prospectively underwent 3DSTE for left atrial (LA) and left ventricle (LV) strain analysis. HCM mutation carriers showed significantly higher LA minimum volume (ml/m(2)) (17 ± 6 vs. 14 ± 4, respectively, P = 0.03) and a significantly lower peak atrial longitudinal strain (PALS) (%), (27 ± 5 vs. 31 ± 7, respectively, P = 0.02) when compared to controls. However, no differences were found in global or regional LV systolic myocardial deformation between both groups. Manifest HCM patients, compared to carriers showed significantly higher LA minimum (27 ± 10 vs. 17 ± 6, respectively, P < 0.001) and maximum volume (42 ± 14 vs. 32 ± 8, respectively, P = 0.007) as well as lower LA ejection fraction (%) (35 ± 8 vs. 47 ± 9, respectively, P < 0.001) and PALS (17 ± 5 vs. 27 ± 5, respectively, P < 0.001). Comparing LV strain, HCM patients showed reduced global longitudinal (-11 ± 4 vs. -16 ± 3, respectively, P < 0.001) and area strain (-35 ± 6 vs. -40 ± 5, respectively, P = 0.005). HCM mutation carriers may be distinguished from healthy subjects using 3DSTE through detection of LA dysfunction that may indicate LV diastolic dysfunction. Further research in a larger study population with gene-specific analysis is warranted for potential clinical usefulness of 3DSTE in family screening for HCM.