We present our experience in the diagnosis, surgical management and long-term follow-up of congenital and acquired osseous–ligamentous abnormalities or pathologies of the craniovertebral junction. The purpose of this study was: (i) to determine the incidence and degree of cervicomedullary compression in pediatric and young adult patients with congenital and acquired abnormalities, and (ii) to correlate cervicomedullary compression with other imaging and clinical factors to determine to what extend cervicomedullary compression is successfully treated with a posterior decompressive procedure, transoral decompression, and medical management. Between January 1995 and December 2004, 26 cases were managed in our department. These patients had: rheumatoid arthritis (RA) (3); traumatic injury (2); congenital basilar impression (5, in 2 cases a posteriorly oriented or retroflexed odontoid); infection (10); craniovertebral junction Pott’s disease (9); os odonteideum (3); condylus tertius (1); and tumor (2). Six of the patients (23.1%) had syringomyelia. Only three (11.3%) were in the pediatric age group. Symptoms and signs included headache (72%), ataxia (38%), lower cranial nerve dysfunction (54%), quadriparesis (44%), hyperreflexia (76%), Hoffman positivity (72%), achilles clonus (72%) nystagmus (33%) and dysphagia (22%). The mean follow-up time was 44 months (range 3–85). Twelve (46.2%) had undergone posterior fossa decompression; seven (26.6%) had ventral decompression. Seven of the patients (26.6%) had medical management. The major morbidity included pharyngeal wound sepsis leading to dehiscence (3.8%), valopharyngeal insufficiency (3.8%), cerebrospinal fluid leakage (3.8%), postoperative macroglossia (3.8%) and inadequate anterior decompression (3.8%). Transient neurological deterioration occurred in two patients (7.6%). Our management paradigm will result in some neurologic improvements and limit the progression of symptoms. Patients with these pathologies are likely to show a good neurologic outcome when treatment, whether with or without surgery, is administered early in the course of the disease.