Aims Cryptogenic stroke (CS) is associated with high rate of recurrences and adverse outcomes at long-term follow-up, especially in light of its unknown etiology that often leads to ineffective secondary prevention. In such scenario, asymptomatic misdiagnosed atrial fibrillation (AF) episodes could play an important pathophysiological role. Some studies have pointed left atrial (LA) and left ventricular (LV) systolic and diastolic dysfunction as surrogate markers of AF. The aim of this study was to evaluate the relationship between echocardiographic parameters of LA and LV function, and the occurrence of AF revealed by continuous electrocardiogram (ECG) monitoring in a cohort of CS patients. Methods and results This is a single-centre prospective cohort study. Seventy-two CS patients with continuous ECG monitoring with insertable cardiac monitor (ICM) underwent transthoracic echocardiography (TTE). TTE was focused on LA and LV function, including both standard and longitudinal strain-derived parameters. All detected AF episodes lasting more than 2 min were considered. Patients with and without AF were homogeneous in all baseline characteristics, except for CHA2DS2-VASc score, which was significantly higher in AF group, and prevalence of hypercholesterolaemia, that was significantly higher in no-AF group. ICM revealed AF in 23 patients (32%), on average 196 days after ICM implantation. Among echocardiographic parameters, LV ejection fraction (LVEF, P = 0.007), LA end systolic area (LAES area, P = 0.006), LA volume index (LAVI, P = 0.008), total LA emptying fraction (LATEF, P = 0.013), E velocity (P = 0.042), pulmonary veins AR duration (P = 0.01), septal and median TDI E/e′ (respectively, P = 0.045 and P = 0.039), peak atrial longitudinal strain (PALS) in 4-chamber and in 2-chamber view (respectively, P < 0.001 and P = 0.011), peak atrial contraction strain (PACS, P < 0.001), LA conduit strain (P = 0.005), and LV longitudinal strain (LVLS, P = 0.001) were significantly associated to the occurrence of AF, suggesting worst atrial function in AF group. Furthermore, multivariable regression analysis revealed that PACS and LV strain were the only echocardiographic parameters independently associated with AF [confidence interval (CI) 95%: 0.48–0.90, P = 0.005 and CI 95%: 0.46–0.95, P = 0.041 respectively]. Conclusions In a cohort of CS patients, continuous ECG monitoring with ICM revealed subclinical AF episodes in about one-third of patients. In such population, LA and LV strain analysis add predictive value for occurrence of AF over clinical and morpho-functional echocardiographic parameters. Impaired booster pump strain and LVLS strain are strong and independent predictors of AF.