Modern functional diagnosis is carried out in a series of steps appropriate to the indications. If a craniomandibular dysfunction or disorder (CMD) is strongly suspected, clinical functional analysis is the first step of the diagnostic cascade. The fundamental elements of this examination have been established for decades. Since the 1990s, new standards have been established requiring an extended clinical exam in which psychosomatic and orthopedic influences are also sought. Computer-based systems are available to evaluate the results and to help correlate the clinical findings with the appropriate diagnoses (CMDfact). The same data can be utilized in new patient information systems and evidence-based expert systems for treatment planning. They can be used in systems for semi-automatic compilation of patient records for referring physicians ("Arztbrief-Assistent CMD"; medical report assistant CMD). The findings from medical imaging have to be checked against the clinical functional analysis. Computer-based systems for this particular application are near completion and clinical use (CMDtomo), while systems for the processing of instrumental findings are being developed (CMD3D). The importance of clinical functional analysis is likely to increase as software-based diagnostic instruments facilitate practitioners' assessments of findings, and this will put them in a similar position to specialist centers where they could consult with colleagues. Keywords: clinical functional analysis, craniomandibular dysfunction, craniomandibular disorder, CMD screening, computer-based documentation, diagnostic software