There is a need to align the mechanical axis of the tibia with the axis of loading for studies involving tibiofemoral compression to interpret results and to ensure repeatability of loading within and among specimens. Therefore, the objectives of this study were (1) to develop a magnetic resonance imaging (MRI)-based alignment method for use with apparatuses applying tibiofemoral joint compression, (2) to demonstrate the usefulness of the method by aligning cadaveric knees in an apparatus that could apply tibiofemoral joint compression, and (3) to quantify the error associated with the alignment method. A four degree-of-freedom adjustable device was constructed to allow determination and alignment of the mechanical axis of the tibia of cadaveric knee joints with the axis of loading of an apparatus applying tibiofemoral joint compression. MRI was used to determine the locations of bony landmarks in three dimensions defining the mechanical axis of the tibia relative to an initial orientation of the four degree-of-freedom device. Adjustment values of the device were then computed and applied to the device to align the mechanical axis of the tibia with the axis of a compressive loading apparatus. To demonstrate the usefulness of the method, four cadaveric knees were aligned in the compressive loading apparatus. The vectors describing the mechanical axis of the tibia and the loading axis of the apparatus before and after adjustment of the four degree-of-freedom device were computed for each cadaveric knee. After adjustment of the four degree-of-freedom device, the mechanical axis of the tibia was collinear with the loading axis of the apparatus for each cadaveric knee. The errors in the adjustment values introduced by inaccuracies in the MR images were quantified using the Monte Carlo technique. The precisions in the translational and rotational adjustments were and respectively. The MR-based alignment method will allow consistent interpretation of results obtained during tibiofemoral compressive studies conducted using the apparatus described in this paper by providing a well-defined loading axis. The alignment method can also be adapted for use with other apparatuses applying tibiofemoral compression.