Background Severe brady-arrhythmias, requiring a permanent pacemaker (PPM), have been sparsely reported in systemic lupus erythematosus (SLE). The aim of this study was to describe the characteristics of such arrhythmias in a defined lupus cohort. Patients and methods The database of the Toronto Lupus Clinic ( n = 1366) was searched for patients who received a PPM. Demographic, clinical, immunological and therapeutic variables along with electrocardiographic (ECG) and echocardiographic findings (based on the last available test prior to PPM) were analyzed. Patients with a PPM (cases) were compared with age-, sex- and disease duration-matched patients without a PPM (controls). Analysis was performed with SAS 9.0; p < 0.05 was considered significant. Results Eighteen patients were identified, 13 (0.95%) with complete atrioventricular block and 5 (0.37%) with sick sinus syndrome. Disease duration at PPM implantation was 22 ± 12 years. Compared to controls, cases had more frequently coronary artery disease, hypertension, dyslipidemia and longer antimalarial (AM) treatment duration. The prevalence of first-degree atrioventricular block, right bundle branch block, left anterior fascicular block and septal hypertrophy was also higher. AM treatment was significantly associated with brady-arrhythmias (OR = 1.128, 95% CI = 1.003-1.267, p = 0.044). Nine patients had prior heart disease and one received a PPM two years after renal transplantation. Eight patients did not have any potential risk factors; prolonged AM therapy (mean 22 years) might have been the cause. Conclusions Apart from known causes, prolonged AM treatment may be associated with severe brady-arrhythmias in SLE. Certain ECG and echocardiographic characteristics may represent indicators of an ongoing damage in the conduction system.