Background Music can evoke strong emotions and thus elicit significant autonomic nervous system (ANS) responses. However, previous studies investigating music-evoked ANS effects produced inconsistent results. In particular, it is not clear (a) whether simply a musical tactus (without common emotional components of music) is sufficient to elicit ANS effects; (b) whether changes in the tempo of a musical piece contribute to the ANS effects; (c) whether emotional valence of music influences ANS effects; and (d) whether music-elicited ANS effects are comparable in healthy subjects and patients with Crohn´s disease (CD, an inflammatory bowel disease suspected to be associated with autonomic dysfunction). Methods To address these issues, three experiments were conducted, with a total of n = 138 healthy subjects and n = 19 CD patients. Heart rate (HR), heart rate variability (HRV), and electrodermal activity (EDA) were recorded while participants listened to joyful pleasant music, isochronous tones, and unpleasant control stimuli. Results Compared to silence, both pleasant music and unpleasant control stimuli elicited an increase in HR and a decrease in a variety of HRV parameters. Surprisingly, similar ANS effects were elicited by isochronous tones (i.e., simply by a tactus). ANS effects did not differ between pleasant and unpleasant stimuli, and different tempi of the music did not entrain ANS activity. Finally, music-evoked ANS effects did not differ between healthy individuals and CD patients.