Patients with calcaneus fractures experience considerable interferences with daily living activities. The quality of anatomical reconstruction is important because of its influence on functional outcome. The aim of this study was to develop an automatic algorithm based on computer tomographic (CT) images to quantify the integrity of calcaneal joint surfaces. Validation of this algorithm was done by assessing intra-individual variations of characteristic joint parameters. Bilateral hind foot CT data of 12 subjects were manually segmented, and 3D models from the calcaneus, talus and cuboid were generated. These models were implemented in a custom-made software to analyse the area, 3D orientations and bone distance of the joint surfaces of the calcaneus. Three joints were detected, and the calculated parameters were compared between right and left hind foot by the evaluation of the directional asymmetry (%DA). The results were statistically analysed with a paired t-test. The median of area (5-7 %DA) of the joint surfaces and the distance between two articulating surfaces (8-9 %DA) showed the greatest intra-individual differences. Median differences in 3D orientation were comparatively low (1-2 %DA). None of these differences was statistically significant. Inter-individual variations among subjects were several magnitudes larger than intra-individual differences. The presented computational tool provides 3D joint-specific parameters of the calcaneus, which enable to describe their respective joint integrity. The results show that only small intra-individual differences within the anatomy exist. Surgical treatment should take place with the aid of CT data from the contralateral side. Thus, a good restoration of the anatomy may be reached. The computational tool assesses the quality of reduction, and may be helpful to evaluate the outcome and quality of operative treatment based on the calculated joint-specific parameters of joint reconstructions in the hind foot.