Dysphagia in motor neuron disease (MND) may lead to dangerous complications such as cachexia and aspiration pneumonia. Functional evaluation of the oropharyngeal tract is crucial for identifying specific swallowing dysfunctions and planning appropriate rehabilitation. As part of a multidisciplinary study on the treatment of dysphagia in patients with neuromuscular diseases, 23 MND patients with different degrees of dysphagia underwent videoflouroscopy, videopharyngolaryngoscopy and pharyngo-oesophageal manometry. The results of the three instrumental investigations were analysed in order (1) to define the pattern of swallowing in MND patients complaining of dysphagia; (2) to evaluate whether subclinical abnormalities may be detected; and (3) to assess the role of videofluoroscopy, videopharyngolaryngoscopy and manometry in the evaluation of MND patients with deglutition problems. Correlations between the instrumental findings and clinical features (age of the patients, duration and severity of the disease, presence and degree of dysphagia) were also assessed. The results of our study showed that: (1) The oral phase of deglutition was compromised most often, followed by the pharyngeal phase. (2) In all patients without clinical evidence of dysphagia, subclinical videofluoroscopic alterations were present in a pattern similar to that found in the dysphagic group. (3) Videofluoroscopy was the most sensitive technique in identifying oropharyngeal alterations of swallowing. Impairment of the oral phase, abnormal pharyngo-oesophageal motility and incomplete relaxation of the upper oesophageal sphincter were the changes most sensitive in detecting dysphagia. Videofluoroscopy was also capable of detecting preclinical abnormalities in non-dysphagic patients who later developed dysphagia. Practical guidelines for the use of instrumental investigations in the assessment and management of dysphagia in MND patients are proposed.