Aims Patients with a history of atrial fibrillation (AF) have previously been shown to have altered atrial conduction, as seen non-invasively using signal-averaged P-wave analysis. However, little is known about the P-wave morphology in patients in the early phases of AF with structurally normal hearts. Methods and results Thirty-six patients with lone AF were included before the age of 40 years (34 ± 4 years, 34 men) and compared with age- and gender-matched control subjects. Standard 12-lead electrocardiogram (ECG) was recorded for at least 10 s. P-wave morphology and duration were estimated using signal-averaged P-wave analysis. Echocardiography was performed in association with the ECG recording. Heart rate (67 ± 13 vs. 65 ± 7 b.p.m., P = 0.800) and PQ-interval (163 ± 16 vs. 164 ± 23 ms, P = 0.629) were similar in AF cases and controls, as was P-wave duration (136 ± 13 vs. 129 ± 13 ms, P = 0.107). The distribution of P-wave morphology differed between the AF cases and controls [33/58/0/8 vs. 75/25/0/0% (Type 1/Type 2/Type 3/atypical), P = 0.001], with a larger proportion of patients with AF exhibiting signs of impaired interatrial conduction. Conclusion A significant difference in P-wave morphology distribution was seen between patients with early-onset, lone paroxysmal AF and age- and gender-matched healthy control subjects. This finding indicates that alterations in atrial electrophysiology are common in the early stage of the arrhythmia, and since it occurs in young patients without co-morbidity may well be the cause rather than the consequence of AF.