Introduction: Left atrium (LA) dilates and its function decreases as a chronic secondary change in hypertrophic cardiomyopathy (HCM). LA strain is a more sensitive measure of LV filling pressure than LA volume and can be used to predict the functional capacity in HCM. Objective: To analyse LA strain in patients with HCM and its correlation with exercise tolerance. Methods: A total of 113 patients with HCM were enrolled. All patients underwent detailed clinical evaluation, 24-hour Holter monitoring, exercise stress testing, two dimensional echocardiography with LA strain analysis using speckle tracking imaging. Assessment of functional capacity was done in terms of metabolic equivalents (METS). HCM patients with METS > 6.0 were included in group A while those with METS ≤ 6.0 were included group B. Correlation of various parameters of LA strain (LASr, LAScd and LASct) was done with functional capacity. Results: Mean age of the study population was 47±10.77 years with majority of them being males (71.9%). Group B patients had significantly lower LASr (12.95 ±8.61% vs 22.16±16%; P<0.001), LAScd (-7.28 ±6.29% vs -12.74±8.40%; P<0.001) and LASct (-7.44 ±4.46 vs -11.19±6.53; P<0.001). Multivariable linear regression analysis reported LASr to be an independent predictor of METs (P = 0.04). LASr was strongest echocardiographic predictor of reduced METS with an AUC of 0.78 (95% CI: 0.68 to 0.88), sensitivity of 71.8% and specificity of 82.9%. Conclusion: LA strain parameters are associated with functional capacity in patients with HCM with lower LA strain values being associated with poor functional capacity.