The prosthetic alignment procedure considers biomechanical, anatomical and comfort characteristics of the amputee to achieve an acceptable gait. Prosthetic malalignment induces long-term disease. The assessment of alignment is highly variable and subjective to the experience of the prosthetist, so the use of machine learning could assist the prosthetist during the judgment of optimal alignment.To assist the prosthetist during the assessment of prosthetic alignment using a new computational protocol based on machine learning.Sixteen transfemoral amputees were recruited for training and validation of the alignment protocol. Four misalignments and one nominal alignment were performed. Eleven prosthetic limb ground reaction force parameters were recorded. A support vector machine with a Gaussian kernel radial basis function and a Bayesian regularization neural network were trained to predict the alignment condition, as well as the magnitude and angle of required to align the prosthesis correctly. The alignment protocol was validated by one junior and one senior prosthetist during the prosthetic alignment of two transfemoral amputees.The support vector machine-based model detected the nominal alignment 92.6 % of the time. The neural network recovered 94.11 % of the angles needed to correct the prosthetic misalignment with a fitting error of 0.51°. During the validation of the alignment protocol, the computational models and the prosthetists agreed on the alignment assessment. The gait quality evaluated by the prosthetists reached a satisfaction level of 8/10 for the first amputee and 9.6/10 for the second amputee.The new computational prosthetic alignment protocol is a tool that helps the prosthetist during the prosthetic alignment procedure thereby decreasing the likelihood of gait deviations and musculoskeletal diseases associated with misalignments and consequently improving the amputees-prosthesis adherence.