Introduction: Wind instrumentalists like clarinetists, may present a muscular hyperactivity on certain groups of the cranio-cervico-mandibular complex, due to their musical activity. Therefore, the use of infrared thermography can be used to assess and characterize the orofacial structures involved in clarinet performance. Aim: The objective of this study was to analyze and record the thermal patterns using the thermographic camera Flir® E60sc to evaluate anatomically and physiologically certain orofacial structures of the cranio-cervical-mandibular complex, such as the masticatory muscles and the region of the temporomandibular joint. Methodology: A sample of 30 clarinetists completed an individual questionnaire composed of two components (musical and clinical history of the participant), and were subjected to a clinical examination. Four thermographic images were taken of the cranio-cervical-mandibular complex at a rest position with frontal, right lateral, left lateral and anterior dentoalveolar components views. Each musician performed a piece of music for an uninterrupted period of 10 min. New thermographic images were captured with the same incidences, after the performance, respecting the same protocol. Results: There were statistically significant differences in the areas corresponding to the left temporal muscle, the orbicularis muscle (labial component), the left and right perioral teguments, as well as in the upper central incisors. There was also statistical evidence regarding the initial and final temperature asymmetries regarding temporal muscle and orbicular muscles (labial and marginal components). Conclusion: Infrared thermography has been shown to be an effective complementary diagnostic tool in the monitorization of the cranio-cervical-mandibular complex of clarinetists.