The autonomic modulation in HIV patients undergoing highly active antiretroviral therapy (HAART) was investigated. The heart rate variability (HRV) was assessed in 13 HIV patients (43+/-2 years) and 10 healthy controls (31+/-5 years) at rest, during exercise, and recovery. All time (standard deviation of NN intervals, SDNN; root mean of squared sum of successive differences, rMSSD; relative number of pairs of adjacent RR intervals differing more than 50 ms, pNN50) and frequency (Low Frequency, LF; High Frequency, HF) HRV components were lower in HIV patients at rest [SDNN (HIV: 44.2+/-3.9 ms vs. CONTROL: 65.5+/-9.8 ms; P=0.04); rMSSD (HIV: 27.2+/-3.6 ms vs. CONTROL: 49.3+/-8.3 ms; P=0.02); pNN50 (HIV: 8.8+/-2.9% vs. CONTROL: 26.5+/-7.0%; P=0.02); LF (HIV: 502.4+/-80.5 ms2 vs. CONTROL: 1302.8+/-446.4 ms2; P=0.04); HF (HIV: 296.4 +/- 62.3 ms2 vs. CONTROL: 986.3+/-280.6 ms2; P=0.01)] and post-exercise [SDNN (HIV: 32.3+/-3.5 ms vs. CONTROL: 55.8+/-5.9 ms; P=0.002); rMSSD (HIV: 17.4+/-3.1 ms vs. CONTROL: 36.6+/-4.6 ms; P=0.002); pNN50 (HIV: 2.9+/-1.2% vs. CONTROL: 14.7+/-3.4%; P=0.001); LF (HIV: 404.9+/-102.6 ms2 vs. CONTROL: 910.1+/-214.2 ms2; P=0.03); HF (HIV: 147.6 +/- 40.1 ms vs. CONTROL: 554.5+/-135.0 ms2; P=0.004)]. No between-group differences were found during exercise (P>0.05 for all comparisons). In conclusion, HIV patients showed impaired autonomic modulation, with reduced parasympathetic activity at rest and during post-exercise recovery.