AIM: To verify the mechanisms of dysphagia in patients in 3 IEM groups. CASE REPORT: We evaluated 3 patients with 3 different diseases by using the protocol of the stomatognathic system AMIOFE (Assessment Protocol Myofunctional with Scores; Felicio and Ferreira, 2008). The evaluation was performed visually and recorded for analysis of the patients, one from each group. Group 1 presented with defects in intermediary metabolism culminating in acute or chronic intoxication, Group 2 exhibited a deficiency in the production or use of energy, and Group 3 had errors in the synthesis or catabolism of complex molecules. The patient in Group 1 had organic aciduria, the patient in Group 2 had mitochondrial disease, and the patient in Group 3 had mucopolysaccharidosis I. The patient in Group 1 did not perform the movements required for structural assessment of the stomatognathic system and refused to swallow. The patient in Group 2 presented poor mobility of the stomatognathic organs and swallowing disorders. The patient in Group 3 showed changes in structural system, poor mobility, and swallowing disorders. CONCLUSION: Evaluation of the 3 patients revealed structural changes and/or poor mobility of the stomatognathic system and dysphagia. Each patient showed changes with differing levels of severity; the speech therapist needs to be aware of these changes to apply appropriate therapy.