Remote adverse effects of local intramuscular botulinum toxin were investigated in a prospective follow-up study. Twenty-six patients with spasmodic torticollis were examined (18 women, eight men, 45 ± 13 years). Respiratory heart rate variation (HRV) was investigated by a computerized method. Different parameters were recorded (beats per minute, coefficient of variation, root mean square successive difference (RMSSD), spectral analysis, difference and quotient between maximum and minimum RR intervals, mean circular resultant). After one intramuscular injection of 12.5 ng botulinum toxin (Porton Products Ltd., England), no significant influence on HRV was seen. After the second injection, a significant attenuation was seen of four parameters (coefficient of variation, Rmax − Rmin, Rmax ÷ Rmin, mean circular resultant) that lasted up to several months. No clinically manifest remote side effects and no cardiac arrhythmia were seen for several months of botulinum toxin treatment. Our investigation proves an effect of local intramuscular botulinum toxin on autonomic cardiac innervation.