Intramedullary instrumentation for femoral component alignment during total knee arthroplasty is readily used. Newer alignment techniques using computer navigation are now available. This study assesses the difference in the sagittal and coronal plane alignments using a cadaveric model with 3 different entry points for intramedullary alignment compared with a navigation system. Seven cadaveric limb's results show that the anterior starting point resulted in recurvatum (-2.2 degrees +/- 1.4 degrees ), the middle starting point resulted in 1.9 degrees +/- 2.2 degrees of flexion, and the posterior starting point in 3.8 degrees +/- 2.6 degrees of flexion compared with the calculated femoral axis by the computer navigation system. When comparing the valgus angle, no statistical difference between any methods resulted (average 5.2 degrees +/- 0.9 degrees valgus). The anterior and posterior starting points were significantly different in the sagittal plane. These data suggest that alignment can be significantly affected by the starting point chosen for intramedullary instrumentation.