Several carpal pathologies are considered to be related to ulnar variance. Recently, computer-aided computed tomography (CT) analysis software was introduced to quantify three-dimensional (3D) carpal alignment with high accuracy and reliability. To determine the association of ulnar variance with 3D carpal alignment and demographics. A wrist of 121 asymptomatic volunteers (69 men, 52 women; mean age = 38 ± 10.4 years) was imaged in the neutral wrist position with cone-beam CT. Computer-aided CT analysis software (Bonelogic), based on segmentation and numerical modelling, was used to define ulnar variance and standardized 3D axes for all carpal bones. The association of ulnar variance with 3D carpal alignment, age of the volunteer, and side and dominance of the imaged wrist was assessed. The mean ulnar variance was -1.6 ± 1.5 mm (range = -5.3 to 2.4 mm). The mean ulnar variance was -1.9 mm and -1.1 mm in men and women (P = 0.007), respectively. Of the imaged 121 wrists, 18 (15%) had positive and 103 (85%) negative ulnar variance. There was no association between ulnar variance and any of the radio- or intercarpal angle values in either the sagittal or coronal plane (ρ = -0.16…0.17, r = -0.13….0.12). The ulnar variance showed no association with side (P = 0.51) or dominance (P = 0.27) of the imaged wrist. 3D carpal alignment is not affected by ulnar variance. The association of ulnar variance with sex may in part explain the difference in reported prevalence of some carpal pathologies, such as ulnar impaction syndrome and Kienböck's disease.