Spinal instrumentation has made significant advances in the last two decades, with transpedicular constructs now widely used in spinal fixation. Pedicle screw constructs are routinely used in thoracolumbar-instrumented fusions, and in recent years, the cervical spine as well. Three-column fixations with pedicle screws provide the most rigid form of posterior stabilization. Surgical landmarks and fluoroscopy have been used routinely for pedicle screw insertion, but a number of studies reveal inaccuracies in placement using these conventional techniques (ranging from 10% to 50%). The ability to combine 3D imaging with intraoperative navigation systems has improved the accuracy and safety of pedicle screw placement, especially in more complex spinal deformities. However, in the authors’ experience with image guidance in more than 1500 cases, several potential pitfalls have been identified while using intraoperative spinal navigation that could lead to suboptimal results. This article summarizes the authors’ experience with these various pitfalls using spinal navigation, and gives practical tips on their avoidance and management.