Background The combination of early transmitral inflow velocity and mitral annular tissue Doppler imaging (E/Em ratio) is widely applied to noninvasively estimate left ventricular (LV) filling pressures. However E/Em ratio has a significant gray zone and its accuracy in patients with heart failure is debated. Left atrial (LA) deformation analysis by speckle tracking echocardiography (STE) was recently proposed as an alternative approach to estimate LV filling pressures. This study aimed at exploring the correlation of LA longitudinal function by STE and Doppler measurements with direct measurements of LV filling pressures in patients with heart failure. Methods A total of 36 patients with advanced systolic heart failure (ejection fraction ≤35%), undergoing right heart catheterization, were studied. Simultaneously to pulmonary capillary wedge pressure (PCWP) determination, peak atrial longitudinal strain (PALS) and mean E/Em ratio were measured in all subjects by two independent operators. PALS values were obtained by averaging all segments (global PALS), and by separately averaging segments measured in the 4-chamber and 2-chamber views. Results Not significant correlation was found between mean E/Em ratio and PCWP (R = 0.15). A close negative correlation between global PALS and the PCWP was found (R = -0.81, p < 0.0001). Furthermore, global PALS demonstrated the highest diagnostic accuracy (AUC of 0.93) and excellent sensitivity and specificity of 100% and 93%, respectively, to predict elevated filling pressure using a cutoff value less than 15.1%. Bland-Altman analysis confirmed this close agreement between PCWP estimated by global PALS and invasive PCWP (mean bias 0.1 ± 8.0 mmHg). Conclusion In a group of patients with advanced systolic heart failure, E/Em ratio correlated poorly with invasively obtained LV filling pressures. However, LA longitudinal deformation analysis by STE correlated well with PCWP, providing a better estimation of LV filling pressures in this particular clinical setting.