Determining and accurately restoring the flexion-extension axis of the elbow is essential for functional recovery after total elbow arthroplasty (TEA). We evaluated the effect of morphological features of the elbow on variations of alignment of the components at TEA. Morphological and positioning variables were compared by systematic CT scans of 22 elbows in 21 patients after TEA. There were five men and 16 women, and the mean age was 63 years (38 to 80). The mean follow-up was 22 months (11 to 44). The anterior offset and version of the humeral components were significantly affected by the anterior angulation of the humerus (p = 0.052 and p = 0.004, respectively). The anterior offset and version of the ulnar components were strongly significantly affected by the anterior angulation of the ulna (p < 0.001 and p < 0.001). The closer the anterior angulation of the ulna was to the joint, the lower the ulnar anterior offset (p = 0.030) and version of the ulnar component (p = 0.010). The distance from the joint to the varus angulation also affected the lateral offset of the ulnar component (p = 0.046). Anatomical variations at the distal humerus and proximal ulna affect the alignment of the components at TEA. This is explained by abutment of the stems of the components and is particularly severe when there are substantial deformities or the deformities are close to the joint.