Object Cervical spine clearance after trauma in children 0–3 years of age is deceptively difficult. Young children may not be able to communicate effectively, and severe injuries may require intubation and sedation. Currently, no published guidelines are available to aid in decision-making in these complex situations. The purpose of this study was to determine whether a safe and effective protocol-driven system could be developed for clearance of the cervical spine in noncommunicative children between 0 and 3 years of age. Methods Children 0–3 years of age, including intubated patients, who were admitted after trauma activation at Primary Children's Medical Center in Salt Lake City or the Children's Hospital of New York from 2002 to 2006 were managed according to a cervical spine clearance protocol. Data were collected in a prospective fashion. Radiographic and clinical methods of clearing the cervical spine, as well as the type and management of injuries, were recorded. Results A total of 2828 pediatric trauma activations required cervical spine clearance during the study period. Of these, 575 (20%) were children ≤ 3 years of age who were admitted to the hospital. To facilitate clearing the cervical spine in these children, plain radiographs (100%), CT studies (14%), and MR images (10%) were obtained. Nineteen ligamentous injuries (3.3%) and 9 fractures/dislocations (1.5%) were detected, with 4 patients requiring operative stabilization (0.7%). No late injuries have been detected. Conclusions The protocol used has been effective in detecting cervical spine injuries in noncommunicative children after trauma. The combination of clinical information and radiographic studies is essential for safely clearing the cervical spine in these complex situations. Clearance of the cervical spine without CT or MR imaging studies is possible in the majority of cases, even in very young patients.