Neonatal brachial plexus palsy (NBPP) is frequently associated with internal rotation contractures of the shoulder as a result of muscle imbalance due to muscle fattening and/or fibrosis which favour the internal rotation of the shoulder. Botulinum toxin A (BTX-A) injection in the subscapularis (SC) muscle could weaken the SC and thereby restore muscle balance. The purpose of this study was to assess the effect of intra muscular injection of BTX-A in the SC on the passive external rotation and the need for external rotation surgery in NBPP patients after BTX-A injection. A prospective comparative study was performed with 93 patients with progressive internal rotation contractures. Al patients underwent an MRI to determine the percentage of the humeral head anterior to the glenoid (PHHA) and glenoid version. Patients younger than 48 months old and with a minimum deformity (PHHA>
=35%) or moderate deformity (PHHA<
35%) were included. Patients with a severe deformity or complete posterior dislocation were excluded. Fifteen consecutive patients were injected with BTX-A (2 U/kg body weight, botox®) at two sites of the SC of the affected shoulder immediately after the MRI under general anesthesia. Seventy eight patients were included as a control group before the new BTX-A treatment was introduced. The passive external rotation was measured pre-MRI and at follow-up. The indication for external rotation surgery was determined after the MRI was performed. No adverse events were observed. Pre-MRI, the mean passive external rotation in adduction in the BTX-A group was −5° (SE 8°) and in the control group 3° (SE 3°). In the BTX-A group, the mean passive external rotation in adduction increased with 53° (95% CI 31°–74°, p<
0.001) compared to the control group. After stratification the beneficial effect of BTX-A was observed in patients with a minimum deformity (54°, 95% CI 37°–71°, p<
0.001), but this was not significant in patients with a moderate deformity (47°, 95% CI −20°−115°, p=0.13) compared to the control group. The patients in the BTX-A group were less frequently indicated for external rotation surgery compared the control group (27% vs. 89%, p<
0.001). The maximum effect of BTX-A injection was observed at a mean follow-up of 3 months (SE 1). The control group was followed for a mean of 7 months (SE 0.4) to observe the natural history of internal rotation contractures. The groups were comparable regarding type of lesion, primary treatment, age, PHHA, glenoid version and passive external rotation pre-MRI (p 0.09–0.74). BTX-A injections in the SC of NBPP patients reduce internal rotation contractures. This effect was mainly observed in patients with a minimum glenohumeral deformity. Restoration of muscle balance could prevent further glenohumeral deformation and could prevent external rotation surgery.