Systemic sclerosis (SSc) is a connective tissue disease characterized by vascular damage and interstizial fibrosis of many organs. Our interest was focused on the evaluation of cardiac autonomic function by measurements of heart rate variability (HRV) and microvascular damage detected by nailfold capillaroscopy (NC) in SSc patients. We examined 25 consecutive outpatients affected by systemic sclerosis and 25 healthy controls. Exclusion criteria were the presence of cardiac disease, hypertension, diabetes mellitus, or neurological diseases. All subjects underwent 24-h ambulatory ECG Holter recording and NC examination. Heart rate variability was evaluated in the time domain, using appropriate software, computing the time series of all normal-to-normal (NN) QRS intervals throughout the 24-h recording period. A semiquantitative rating scale was adopted to score the NC abnormalities, as well as a rating system for avascular areas and morphological NC patterns. In SSc patients, HRV analysis showed significantly lower values of SDNN (standard deviation of all NN intervals) (p=0.009), SDANN (standard deviation of the averages of NN intervals in all 5-min segments of the entire recording) (p=0.01), and pNN50 (the percentage of adjacent NN intervals that differed by more than 50 ms) (p=0.02), compared to the control group. These parameters in SSc patients significantly decreased with the worsening of semiquantitative capillaroscopy score. In conclusion, an abnormal autonomic nervous control of the heart might contribute to identify subclinical cardiac involvement in SSc patients. The coexistence of autonomic dysfunction with a more severe microvascular damage could be considered a potential prognostic tool in the identification of those patients particularly at risk for cardiac mortality.