The aim of this study was to evaluate the correlation between patient complaints, clinical diagnosis of temporomandibular disorder (TMD) based on the diagnostic criteria for TMD, and morphology of the mandibular condyle obtained by cone-beam computed tomography (CB-CT). Data were collected from 40 patients. The anatomy of the mandibular condyle was assessed using CB-CT, the diagnosis of TMD according to diagnostic criteria for TMD, and patients' complaints was registered at the appointment. Data were explored and all statistical references were completed in bicaudal tests, with 95% confidence level (α=0.05). The Chi-squared test was used with Bonferroni correction (z-tests). Main complaints found were grouped as muscular, articular, muscular and articular, or headache and articular symptoms. Clinical diagnosis of TMD involved myalgia, local myalgia, myofascial pain, myofascial pain with reference, myofascial pain with arthralgia, arthralgia, or disc displacement with reduction. At least one joint showed condylar flattening, erosion, sclerosis, or osteophytes. No correlation was observed between main complaints, clinical diagnosis, and morphology of the mandibular condyle in all comparisons. The findings suggest that due to the absence of clinical and morphological correlation, CB-CTs should be requested only in specific cases, when doubt remain after careful TMD diagnosis, to avoid their over-indication.