Studies report that Lisfranc injury is more common than thought. Several imaging methods for assessing the stability of Lisfranc injury have been described but many are impossible to standardize and not accurate enough. To present a three-dimensional (3D) method for analyzing the changes in the joint space width of the midfoot joint and the joints of the medial part of the Lisfranc complex in healthy individuals. Non-weightbearing and weightbearing cone-beam computed tomography (CBCT) images of 11 healthy feet were acquired and analyzed with 3D software. The mean range of joint space width changes of each joint was computed from the changes in individual image pairs. 3D analysis software was used to analyze the medial part of the Lisfranc complex. In this sample of healthy feet, the changes in the joint spaces in the medial part of Lisfranc complex, calculated with 3D analysis software, was less than 0.6 mm. The distance between bones increased or decreased, depending on which part of the joint surface the measurements were taken. In this study, we present a 3D analysis method to evaluate midfoot joint space width changes. Our analysis revealed that in healthy feet there are only minimal changes in the joint space width between weightbearing and non-weightbearing indicating minimal movement of the midtarsal joints. The 3D analysis of weightbearing CBCT data provides a promising tool for analyzing the small midfoot joints in a variety of conditions.