We used computerized simulations with 3-dimensional models of 20 cadaver femora, calculated from computed tomographic scans, and a model of a rod measuring 200 x 5 mm to study femoral alignment accuracy for unicompartmental knee arthroplasty via minimally invasive reconstruction. The anatomical axis and insertion site were identified on each femur. A simulation of all feasible flexion-extension and varus-valgus orientations was performed. The average rod orientation was 3.2 degrees flexion and 2.5 degrees valgus. The range of orientation was 3.2 degrees extension to 9.7 degrees flexion and 4.5 degrees varus to 8.9 degrees valgus. The study suggests that a short narrow intramedullary rod inserted according to the manufacturer's specifications does not accurately find the anatomical axis and may lead to poor alignment of the femoral prosthesis. Given our finding of consistent bias toward excessive flexion and valgus alignment, we recommend that the operating surgeon carefully plan the insertion point of the intramedullary rod during surgery to compensate for this bias.