Traditionally, cephalometric analysis has been limited to data determined from two-dimensional (2-D) cephalograms. With imaging facilities such as CT and biplanar radiography now available, the natural extension has been towards the use of three-dimensional (3-D) coordinate positions of landmarks for comparative purposes. While these data have been potentially available for several years, the accurate and reproducible extraction of anatomic landmarks suitable for comparative purposes has been limited. This paper presents results of the application of traditional comparative techniques to well determined 3-D coordinate data acquired from biplanar radiography and CT for a patient with Treacher Collins syndrome and further provides a comparison with the technique of strain analysis, often referred to as finite element analysis, which has been applied recently to craniofacial data. Comparisons of distances and angles between landmarks, landmark coordinate positions, and strains of the patient relative to experimental reference standards reveal that the essential skeletal features of Treacher Collins syndrome have been identified and quantified by the analysis techniques. Further, a measure of the significance of the deviations has been determined by comparisons with the experimental reference standards.