Heart rate variability (HRV) is reduced in patients with chronic obstructive pulmonary disease (COPD). However, the relationships among HRV and characteristics of COPD are unknown. The aim of this study was to characterize HRV in patients with COPD and to verify the correlation of HRV measured during rest with disease severity and pulmonary, muscular, and functional impairment. Thirty-one patients with COPD (16 male; 66 ± 8 years; BMI = 24 ± 6 kg/m2; FEV1 = 46 ± 16% predicted) without severe cardiac dysfunction were included. HRV assessment was performed by the head-up tilt test (HUTT), and the main variables used for analysis were SDNN index, LF/HF ratio, and R-R intervals. Other tests included spirometry, bioelectrical impedance, cardiopulmonary exercise test, 6-minute walk test, respiratory and peripheral muscle force, health-related quality of life and functional status questionnaires, and objective quantification of physical activity level in daily life with the DynaPort® and SenseWear® armband activity monitors, besides calculation of the BODE index. There was a statistical difference in all variables of HRV between the HUTT positions (lying and standing). There was no correlation of HRV with BODE index or FEV1. Out of the BODE index, just the BMI was correlated with SDNN and R-R intervals (r = 0.44; p < 0.05 and r = 0.37; p < 0.05, respectively). There was correlation between HRV reduction and a lower level of physical activity in daily life, besides worse health-related quality of life, functional status, and respiratory and peripheral muscle force. Cardiac autonomic function of patients with COPD is not related to disease severity but mainly to the level of physical activity in daily life.