The first carpometacarpal (CMC) joint, located at the base of the thumb and formed by the junction between the first metacarpal and trapezium, is a common site for osteoarthritis of the hand. The shape of both the first metacarpal and trapezium contributes to the intrinsic bony stability of the joint, and variability in the morphology of both these bones can affect the joint’s function. The objectives of this study were to quantify the morphological variation in the complete metacarpal and trapezium and determine any correlation between anatomical features of these two components of the first CMC joint. A multi-object statistical shape modelling pipeline, consisting of scaling, hierarchical rigid registration, non-rigid registration and projection pursuit principal component analysis, was implemented. Four anatomical measures were quantified from the shape model, namely the first metacarpal articular tilt and torsion angles and the trapezium length and width. Variations in the first metacarpal articular tilt angle (− 6.3° <
θ
< 12.3°) and trapezium width (10.28 mm <
< 11.13 mm) were identified in the first principal component. In the second principal component, variations in the first metacarpal torsion angle (0.2° <
α
< 14.2°), first metacarpal articular tilt angle (1.0° <
θ
< 6.4°) and trapezium length (12.25 mm <
< 17.33 mm) were determined. Due to their implications for joint stability, the first metacarpal articular tilt angle and trapezium width may be important anatomical features which could be used to advance early detection and treatment of first CMC joint osteoarthritis.