AIM: To evaluate clinical significance of heart rate variability (HRV) in patients with systemic lupus erythematosus (SLE). MATERIAL AND METHODS: HRV was investigated by means of time-domain analysis of 24 hour ambulatory ECG of 122 SLE patients under 55 years of age and 32 age-matched healthy controls. In addition to clinical manifestations and activity of SLE, we assessed the presence of basic conventional cardiovascular risk factors (hypertension, smoking, body mass index, dyslipidemia), performed common carotid duplex scanning with measurement of intima-medial thickness (IMT). Inflammatory markers (ESR, CRP, IL-6) were assessed in all the patients. RESULTS: Significantly lower HRV and the trend to tachycardia were detected in SLE patients when compared to the control group. There was a significant positive correlation between HRV and a cumulative dose of cyclophosphamide, a high density lipoprotein cholesterol level, a negative correlation between HRV and cumulative dose of azathioprine, standard risk factors (hypertension, smoking, body mass index, triglyceride level), markers of inflammation (ESR, CRP, IL-6) and IMT. CONCLUSION: Measurement of HRV in combination with routine cardiovascular risk factors and level of inflammatory markers can be used for identification of subjects at risk for faster progression of atherosclerosis in SLE patients.