An algorithm for automatic spinal pedicle screw planning is reported and evaluated in simulation and first clinical studies. A statistical atlas of the lumbar spine (N = 40 members) was constructed for active shape model (ASM) registration of target vertebrae to an unsegmented patient CT. The atlas was augmented to include 'reference' trajectories through the pedicles as defined by a spinal neurosurgeon. Following ASM registration, the trajectories are transformed to the patient CT and accumulated to define a patient-specific screw trajectory, diameter, and length. The algorithm was evaluated in leave-one-out analysis (N = 40 members) and for the first time in a clinical study (N = 5 patients undergoing cone-beam CT (CBCT) guided spine surgery), and in simulated low-dose CBCT images. ASM registration achieved (2.0 ± 0.5) mm root-mean-square-error (RMSE) in surface registration in 96% of cases, with outliers owing to limitations in CT image quality (high noise/slice thickness). Trajectory centerlines were conformant to the pedicle in 95% of cases. For all non-breaching trajectories, automatically defined screw diameter and length were similarly conformant to the pedicle and vertebral body (98.7%, Grade A/B). The algorithm performed similarly in CBCT clinical studies (93% centerline and screw conformance) and was consistent at the lowest dose levels tested. Average runtime in planning five-level (lumbar) bilateral screws (ten trajectories) was (312.1 ± 104.0) s. The runtime per level for ASM registration was (41.2 ± 39.9) s, and the runtime per trajectory was (4.1 ± 0.8) s, suggesting a runtime of ~(45.3 ± 39.9) s with a more fully parallelized implementation. The algorithm demonstrated accurate, automatic definition of pedicle screw trajectories, diameter, and length in CT images of the spine without segmentation. The studies support translation to clinical studies in free-hand or robot-assisted spine surgery, quality assurance, and data analytics in which fast trajectory definition is a benefit to workflow.