The purpose of this work is to analyze the effect of selective atrial coronary artery occlusion on heart rate variability (HRV). Twelve-hour, Holter recording were studied in 109 patients undergoing elective percutaneous transluminal coronary angioplasty (PTCA) of the right or circumflex coronary artery. Accidental atrial branch occlusions (ABO) were found in 17 patients at the end of the interventions. R-R intervals from sinus origin were used to calculate standard time and frequency domain and fractal HRV indices. Fractal properties were measured by the exponent a1, using detrended fluctuation analysis (DFA) of the R-R series. During the first 10 minutes immediately after PTCA, SDNN was significantly lower in ABO patients respect to non-ABO (32.5±16.0 vs. 49.5±28.6 ms, p = 0.016), showing a reduced autonomic response. Fractal index values a1 were similar in both groups. The 12-hour RR interval series showed an averaged HR of 66±9 bpm in patients with ABO and 63±9 bpm in patients without ABO (p=0.16), and no significant differences were found in the analyzed HRV indices. A higher incidence of atrial tachycardia (41% vs. 15%, p=0.02) and atrial fibrillation (2 ABO vs. 0 non-ABO, p=0.025) was found in patients with ABO. Acute atrial ischemia can lead to a global decrease in the autonomic response that recovers after several minutes and may be associated with atrial arrhythmias.