The aim of this study was to evaluate spinal accessory nerve function after functional neck dissection (FND) and radical neck dissection (RND) by monitoring the nerve with electromyographic (EMG) examinations. A prospective, double-blind, clinical study was undertaken in 21 patients (42 neck side dissections) operated on for head and neck malignant diseases, separated into two groups: 10 neck sides in the RND group and 32 neck sides in the FND group. Electromyographic examinations were performed pre-operatively and post-operatively in the third week and third and ninth months. Additionally, a questionnaire, modified from the neck dissection impairment index, was applied to all the patients in order to assess shoulder function in the ninth post-operative month. All patients had maximum EMG scores pre-operatively. Following the operation, motor amplitudes decreased in both groups. At the third post-operative month, amplitudes decreased to their lowest values. As expected, the decreases in amplitude and EMG score were more prominent in the RND group. Following reinnervation, the amplitudes of the trapezius motor response increased in the FND group but never reached pre-operative values (during the time of follow up). The FND group scores for pain, neck and shoulder stiffness, and disability in heavy object lifting, light object lifting and reaching overhead were significantly lower than those of the RND group. In FND, one aims to preserve anatomically the spinal accessory nerve, and it is presumed to be intact after the procedure. However, using EMG nerve function monitoring, our study revealed that profound spinal nerve injury was detected immediately after FND surgery, which tended to improve over subsequent months but had not regained its original function by the end of the ninth post-operative month.