Background Stroke is often unexplained in younger adults, although it is often associated with a patent foramen ovale (PFO). The reason for the association is not fully explained, and mechanisms other than paradoxical embolism may be involved. Young stroke patients with PFO have more atrial vulnerability than those without PFO. It is plausible that stretching of the interatrial septum may disrupt the interatrial conduction pathways causing interatrial block (IAB). IAB is associated with atrial fibrillation, dysfunctional left atria and stroke. Methods Electrocardiogram (ECG) characteristics of prospectively recruited young patients (≤55 years of age) with unexplained stroke (TOAST and A-S-C-O) were compared with control data. All stroke cases underwent bubble contrast transthoracic and transoesophageal echography. IAB was defined as a P-wave duration of ≥110 ms. ECG data were converted to electronic format and analysed in a blind manner. Results Fifty-five patients and 23 datasets were analysed. Patients with unexplained stroke had longer P-wave duration (p = 0.013) and a greater prevalence of IAB (p = 0.02) than healthy controls. Case status was an independent predictor of P-wave duration in a significant multivariate model. There was a significant increase in the proportion of cases with a PFO with IAB compared with cases without PFO and with controls (p = 0.005). Conclusions Young patients with unexplained stroke, particularly those with PFO, exhibit abnormal atrial electrical characteristics suggesting atrial arrhythmia or atrial dysfunction as a possible mechanism of stroke.