The postnatal craniofacial development is determined by exogenous and endogenous factors that may result in morphological and functional muscle changes and influence the dentoskeletal region in terms of a physiologic or dysgnathic development. Using functional appliances, efforts are made to treat skeletal malocclusions through targeted exercise and to prevent an undesirable development of the dentition and the craniofacial structures. However, the success of the treatment and the stability of the outcome are not always adequate. To illustrate the treatment processes, clinically relevant measures for diagnosing muscle function and morphology have been developed in recent years. Electromyographic investigations and bite-force measurements show an excessively high variability and the histologic examinations applied to date are restricted in their suitability for analysis of the human masticatory muscles. Animal experimental studies have meanwhile succeeded in simulating functional jaw orthopedics and in demonstrating muscle remodeling processes at the genetic level. Despite some invasiveness, the time and the small quantity of muscle tissue involved permit molecular biological measuring in the orofacial system.