Background Left atrium (LA) in patients with hypertrophic cardiomyopathy (HC) has been known to have an increased size and decreased contractile function. The purpose of this study was to investigate LA and left ventricular (LV) volume change and function with real-time 3-dimensional (3D) echocardiography and to investigate association between LA and LV function in HC. Methods We performed real-time 3D echocardiography on 26 patients with HC and on 15 control subjects. LA and LV time-volume curves were obtained from real-time 3D echocardiography and the maximal slope of the time-volume curve was expressed as dV/dt. LA active emptying fraction was calculated as: [(precontraction LA volume − minimal LA volume)/precontraction LA volume] × 100. Results The maximal LA volume index was larger, and LA active emptying fraction was lower, in those with HC than control subjects (50.1 ± 15.9 vs 30.1 ± 6.8 mL/m 2 and 33.3 ± 13.7 vs 40.4 ± 8.6%, both P < .05). LA active emptying fraction showed a negative correlation with precontraction LA volume ( r = −0.64, P < .01) in HC. Patients with HC showed decreased LV early diastolic dV/dt compared with control subjects (0.10 ± 0.05 vs 0.14 ± 0.04 mL/ms, P < .05). LA passive and active emptying dV/dt were correlated with LV early and late diastolic dV/dt, respectively ( r = 0.47 and r = 0.48, both P < .05). Conclusion Our 3D echocardiographic study showed that increased LA volume was related to decreased LA contraction in HC. LA passive emptying was related to LV relaxation whereas LA active contraction was related to LV stiffness.