More and more often do we see patients with pain in the joints and in the muscles seeking orthodontic treatment. Pain, muscle soreness, limited range of motion, the inability to chew because of pain are some of the most frequent complaints of those patients. A comprehensive functional analysis and a complete diagnosis are crucial in these cases.The aim of this lecture is to present the diagnostical protocol I use in my clinical practice for these types of cases as well as the treatment strategies and treatment sequence that allows us to get to a healthy and stable result.