Cardiovascular disease is among the leading causes of mortality in chronic obstructive pulmonary disease (COPD). Nonlinear heart rate variability (NHRV) measures are markers and predictors of cardiovascular disease, particularly arrhythmias. Our aim was to investigate NHRV in patients with COPD and changes after pulmonary rehabilitation. 20-minute ECGs were used to compare NHRV (a) in 45 healthy individuals and 31 patients with COPD and (b) in 16 patients who completed rehabilitation versus 13 age- and sex-matched control patients. We studied detrended fluctuation analysis (DFA1, DFA2), fractal dimension (low, high, average FD) and sample entropy. Compared to healthy individuals, patients with COPD had lower DFA1 (p=.038). During rehabilitation high FD decreased (p=.018) and DFA2 increased (p=.043). Cluster analysis displayed an increase of DFA1 in the rehabilitation cluster with DFA1 values below 1 (p=.032). NHRV reflects altered autonomic regulation in patients with COPD. Reduced DFA1 in patients with COPD implies a stronger pro-arrhythmic substrate and altered parasympathetic modulation.