Hyperhidrosis is a common disorder that may have a severe impact on quality of life. The aim of this study was to investigate the clinical effect of two novel botulinum toxins, Xeomin®, a type A botulinum toxin, and Neuro-bloc®, a type B botulinum toxin, in the treatment of axillary and palmar hyperhidrosis. A total of 84 patients, 58 with axillary and 26 with palmar hyperhidrosis, were included in this open study. Axillae were injected with 107 ± 22 U Xeomin® and palms were injected with 213 ± 19 U Xeomin® and 264 ± 60 U Neurobloc® over the thenar eminences to avoid muscle weakness. At follow-up 3 weeks post-treatment, all patients treated for axillary hyperhidrosis reported satisfaction in self-ranking, evaporation decreased > 40%, and Dermatology Life Quality Index (DLQI) score improved from 12.0 to 1.7 (p < 0.05). In the palmar group 95% were satisfied, evaporation decreased > 50% and DLQI score improved from 10.3 to 1.2 (p < 0.05). Only one patient in the palmar group experienced muscle weakness. In conclusion, Xeomin® has an excellent effect on axillary hyperhidrosis and in combination with Neurobloc® on palmar hyperhidrosis. Neurobloc® may be an option for use in the treatment of palmar hyperhidrosis in order to minimize muscular side-effects.