Background There are no data on the influence of disease severity and cardiac autonomic tone on ventricular repolarization and dispersion in 24-hour Holter monitoring in systemic lupus erythematosus (SLE). Methods Consecutive 92 SLE and 51 healthy subjects were studied. The standard 12-lead electrocardiography (ECG), Holter monitoring with heart rate turbulence (HRT) and QT, Tp-e and Tp-e/QT ratio assessment (including corrected values) were performed. Subjects with conditions causing repolarization abnormalities or insufficient number of beats suitable for QT evaluation were excluded (17 SLE and 8 controls). Results Finally, 75 SLE and 43 sex- and age-matched controls were included to the study. In SLE patients, the median disease severity score (Systemic Lupus International Collaborating Clinics/American College of Rheumatology Damage Index (SLICC/ACR-DI)) was 3.0. The mean values of QTc, cTp-e and cTp-e/QTc were significantly higher in SLE patients than in controls. QTc ≥ 460 ms was observed in 18.7% of patients using standard ECG and in 58.7% using Holter monitoring. With Holter monitoring, patients with SLICC/ACR-DI >3.0 presented longer QTc than those with SLICC/ACR-DI ≤3.0 (418±15 vs. 409 ± 16, p = 0.04), while cTp-e and cTp-e/QTc values were similar. Patients with abnormal HRT presented longer cTp-e and higher cTp-e/QTc than those with normal HRT (92 ± 52 vs. 71 ± 16 ms, p = 0.04; 0.244 ± 0.126 vs. 0.187 ± 0.035, p = 0.03), while QTc values were similar. No differences in QT and Tp-e parameters were observed according to disease duration. Conclusion In SLE patients, Holter monitoring revealed QTc prolongation more frequently than standard ECG. Longer QTc values were observed in patients with more advanced disease, while increased cTp-e and cTp-e/QTc were related to cardiac autonomic dysfunction expressed by abnormal HRT.