Phantom-limb pain (PLP) is a phenomenon that may appear among people with amputation. Some studies reveal that 70% of people with amputation experience PLP years postamputation. There is a lack of scientific evidence about the cause of PLP. It has been hypothesized that the autonomic nervous system (ANS) could be involved in the mechanism that triggers PLP, but this hypothesis remains unclear. The aim of this study was to correlate ANS function, through heart rate variability (HRV) analysis, with PLP in adult males with amputation. The study population comprised 35 subjects, with 27 reporting PLP often or always. The rest of the subjects did not report any PLP. In order to calculate linear and nonlinear parameters of HRV, all subjects underwent 10 min of resting heart rate monitoring. The study did not find correlations between HRV parameters and PLP. Most of the subjects showed decreased values in linear parameters of HRV while nonlinear values were normal. HRV is not implicated in PLP. Linear and nonlinear methods for HRV analysis might reflect different physiological phenomena; while linear values place people with amputation at cardiovascular risk, nonlinear values indicate normality.