Recently, botulinum toxin type B (BT-B) has become available to treat muscle hyperactivity in cervical dystonia (CD). When we started the clinical use of BT-B, we noticed a side effect profile not seen with botulinum toxin type A (BT-A) before. Altogether 30 consecutive patients were included in this open controlled study. 24 patients were treated for CD with 11,310 ± 2,616 mouse units (MU) of BT-B (NeuroBloc<sup>®</sup>) and 6 for focal hyperhidrosis (HH) with 4,000–10,000 MU. In 5 of them, BT-A (Botox<sup>®</sup>) was used additionally for comparison of effectiveness. In CD, side effects consisted of dryness of mouth (total 21, duration 4.4 ± 2.0 weeks, 10 severe, 7 moderate, 4 mild), accommodation difficulties (7), conjunctival irritation (5), reduced sweating (4), swallowing difficulties (3), heartburn (3), constipation (3), bladder voiding difficulties (2), head instability (1), dryness of nasal mucosa (1) and thrush (1). In HH, side effects consisted of accommodation difficulties (4), dryness of mouth (2) and conjunctival irritation (1). Autonomic side effects occur far more often after BT-B than after BT-A. Their localization suggests systemic BT-B spread. BT-B should be applied carefully in patients with pre-existent autonomic dysfunction, additional anticholinergic treatment and in conditions where anticholinergics are contraindicated.