Atrial fibrillation (AF) is an important arrhythmia in hypertrophic cardiomyopathy (HCM). We aimed to explore whether a complex evaluation of the left ventricle (LV) using modern echocardiography techniques, in addition to the left atrium (LA boosts), could improved the probability of AF diagnosis. Standard echocardiography, 2D and 3D speckle tracking, were performed for LA and LV evaluation in HCM patients and healthy volunteers. Of 128 initially qualified HCM patients, 60 fulfilled included criteria, from which 43 had a history of AF, and 17 were without AF. LA volume index and peak strain, LV ejection fraction, and strains were significant predictors of AF. In addition, 2D global longitudinal strain (GLS) for LV at cut off −16% turned out to be the most accurate predictor of AF (OR 48.00 [95% CI 2.68–859.36], p = 0.001), whereas the combination of LA peak strain ≤ 22% and LV GLS ≥ −16% had the highest discriminatory power (OR 76.36 [95% CI 4.13–1411.36], p = 0.001). AF in HCM patients seems to be LA as well as LV disease. Revealing lower strain for LV, in addition to lower LA strain, may have an important impact on accurate characteristics of HCM patients with AF history.