Objective <p>Accurate assessment of foot and ankle alignment through clinical measurements is essential for diagnosing deformities, treatment planning, and monitoring outcomes. The traditional 2D radiographs fail to fully represent the 3D complexity of the foot and ankle. In contrast, weight-bearing CT provides a 3D view of bone alignment under physiological loading. Nevertheless, manual landmark identification on WBCT remains time-intensive and prone to variability. This study presents a novel AI framework automating foot and ankle alignment assessment via deep learning landmark detection.</p> Materials and methods <p>By training 3D U-Net models to predict 22 anatomical landmarks directly from weight-bearing CT images, using heatmap predictions, our approach eliminates the need for segmentation and iterative mesh registration methods. A small dataset of 74 orthopedic patients, including foot deformity cases such as pes cavus and planovalgus, was used to develop and evaluate the model in a clinically relevant population. The mean absolute error was assessed for each landmark and each angle using a fivefold cross-validation.</p> Results <p>Mean absolute distance errors ranged from 1.00&#xa0;mm for the proximal head center of the first phalanx to a maximum of 1.88&#xa0;mm for the lowest point of the calcaneus. Automated clinical measurements derived from these landmarks achieved mean absolute errors between 0.91° for the hindfoot angle and a maximum of 2.90° for the Böhler angle.</p> Conclusion <p>The heatmap-based AI approach enables automated foot and ankle alignment assessment from WBCT imaging, achieving accuracies comparable to the manual inter-rater variability reported in previous studies. This novel AI-driven method represents a potentially valuable approach for evaluating foot and ankle morphology. However, this exploratory study requires further evaluation with larger datasets to assess its real clinical applicability.</p>