Background: Stemless shoulder arthroplasty (SSA) is used to anatomically reconstruct proximal humerus geometry and preserve proximal humerus bone stock. The current literature lacks 3D-analysis of pre- and postoperative proximal humeral anatomy after SSA. The aim of this study was to prospectively analyze the humeral head anatomy using a computer-assisted topography mapping technique after SSA in relation to the preoperative status and the contralateral (not affected) side. Methods: Twenty-nine patients (mean age: 63.5 +/- 11.7 years) affected by primary shoulder osteoarthritis and treated with SSA were included. Preoperative and postoperative CT scans of the affected and contralateral sites were analyzed regarding joint geometry. Clinical outcome was assessed by Constant and Disabilities of the Arm, Shoulder and Hand (DASH) score shortly before and one year after surgery. Results: Clinical outcome improved significantly. No correlation between clinical outcome and the evaluated anatomical parameters was found. There was a significant decrease of the humeral head height (p < 0.01) and radius (p = 0.03) in the preoperative versus the postoperative joint geometry. The comparison to the contralateral site showed also a significant decrease of the humeral head height (p < 0.01). All other parameters showed no significant differences. Conclusion: Proximal humeral anatomy can be almost anatomically reconstructed by SSA. Solely the humeral head height differs significantly to the preoperative as well as contralateral morphology.