Randomized clinical trials are recognized as providing the most rigorous evidence of treatment efficacy. For temporomandibular disorders, randomized clinical trails have been used to evaluate the efficacy of low-cost occlusal appliances or the adjunct use of cognitive behavioral interventions. However, noncompliance with treatment regimens and losses to follow up are common randomized clinical trial protocol violations that compromise the desired rigor or the trial. At times it is not clear to the investigator how to deal with these issues during the trial and at the data analysis phase. Often treatment efficacy is based on the compliant subjects, subjects who may no longer represent randomized groups or yield the desired fair estimate of treatment efficacy. This study focuses on management of compliance issues, the description and collection of data needed to obtain a more accurate assessment of treatment efficacy, and results particularly relevant to actual clinical practice and patient care decisions. These are applied to a randomized clinical trial evaluating the efficacy of a cognitive-behavioral intervention for temporomandibular disorders.