A computer-implemented method of calculating leg length discrepancy of a patient, the method comprising: using a computer to receive patient bone data associated with a lower body of the patient, the lower body comprising a first side and a second side, the first side comprising a first portion of a pelvis, a first femur, a first tibia, and a first distal extremity, the second side comprising a second portion of the pelvis, a second femur, a second tibia, and a second distal extremity; using the computer to identify anatomical landmarks in the patient bone data, the anatomical landmarks comprising a first proximal landmark and a first distal landmark associated with the first side and a second proximal landmark and a second distal landmark associated with the second side; using the computer to orient the first proximal landmark and the second proximal landmark relative to each other and an origin in a computer coordinate system; characterized by the steps of using the computer to align a first axis associated with the first femur and a second axis associated with the second femur with a longitudinal axis extending in a distal-proximal direction in the computer coordinate system, the first axis comprising a first femoral mechanical axis defined between a first femoral head center of the first femur and a first knee center, and the second axis comprising a second femoral mechanical axis defined between a second femoral head center of the second femur and a second knee center, wherein the first and second distal landmarks are adjusted according to the alignment of the first and second axes, wherein the first tibia and the first distal extremity have a first alignment relative to the first femur that is unchanged when the first and second axes are aligned, and wherein the second tibia and the second distal extremity have a second alignment relative to the second femur that is unchanged when the first and second axes are aligned; using the computer to calculate the leg length discrepancy based on a first distance between the first proximal landmark and the first distal landmark and a second distance between the second proximal landmark and the second distal landmark; and using the computer to display at least one of the leg length discrepancy or a portion of the patient bone data on a display screen. using a computer to receive patient bone data associated with a lower body of the patient, the lower body comprising a first side and a second side, the first side comprising a first portion of a pelvis, a first femur, a first tibia, and a first distal extremity, the second side comprising a second portion of the pelvis, a second femur, a second tibia, and a second distal extremity; using the computer to identify anatomical landmarks in the patient bone data, the anatomical landmarks comprising a first proximal landmark and a first distal landmark associated with the first side and a second proximal landmark and a second distal landmark associated with the second side; using the computer to orient the first proximal landmark and the second proximal landmark relative to each other and an origin in a computer coordinate system; characterized by the steps of using the computer to align a first axis associated with the first femur and a second axis associated with the second femur with a longitudinal axis extending in a distal-proximal direction in the computer coordinate system, the first axis comprising a first femoral mechanical axis defined between a first femoral head center of the first femur and a first knee center, and the second axis comprising a second femoral mechanical axis defined between a second femoral head center of the second femur and a second knee center, wherein the first and second distal landmarks are adjusted according to the alignment of the first and second axes, wherein the first tibia and the first distal extremity have a first alignment relative to the first femur that is unchanged when the first and second axes are aligned, and wherein the second tibia and the second distal extremity have a second alignment relative to the second femur that is unchanged when the first and second axes are aligned; using the computer to calculate the leg length discrepancy based on a first distance between the first proximal landmark and the first distal landmark and a second distance between the second proximal landmark and the second distal landmark; and using the computer to display at least one of the leg length discrepancy or a portion of the patient bone data on a display screen.