In hypertrophic cardiomyopathy (HCM), we often hear loud atrial sounds (S(4)) due to atrial contribution to impaired diastolic ventricular filling. But loudness of S(4) fluctuates according to diastolic hemodynamics. To investigate the reliability of S(4) as a parameter of diastolic filling disturbances in HCM, we studied the correlation between the amplitude of S(4) and mitral inflow velocities using 59 patients with HCM (mean age was 52.8 years). The subjects were divided into two groups based on the amplitude of S(4) on the low frequency phonocardiogram. Group I consisted of 32 patients with large S(4) (amplitude >3 cm) and group II of 27 patients with small S(4) (amplitude <1.5 cm). The left atrial dimension was significantly smaller in group I than in group II (37.8 ± 9.8 vs. 42.7 ± 7.1 mm; p < 0.05). The peak velocity of the early diastolic filling (E) was significantly lower in group I that in group II (45.7 ± 8.9 vs. 52.1 ± 13.0 cm/s; p < 0.05), the peak filling velocity of the atrial contraction period (A) was significantly higher in group I than that in group II (47.5 ± 9.0 vs. 41.4 ± 12.1 cm/s; p < 0.05) and the ratio A/E was significantly larger in group I than that in group II (1.1 ± 0.17 vs. 0.82 ± 0.19; p < 0.001). In conclusion, group I showed larger atrial sounds and more severe impairment of the early diastolic filling which was compensated by more forceful atrial contraction compared with group II. The magnitude of S(4) reflects the left atrial function and the late diastolic filling dynamics due to atrial contraction.