The craniocervical junction (CCJ) comprehends the brainstem, proximal cervical spinal cord and cerebelar structures and is subjected to several congenital anomalies and anatomic variations. Although the morphological abnormalities are present at birth, many patients develop symptoms after third and fourth decades. Magnetic Ressonance Imaging (MRI) analyses were performed for 61 patients with these malformations towards discriminating the degree of compression, elevated signal in fluid sensitive sequences and presence of syringomyelia. The severity of skeletical disturbances correlated with the degree of neural tissue damage, with shorter base skull (represented by basilar hypoplasia) and greater basilar invagination (elevation of odontoid tip) correlating with compression and signals of tissue injury. The small posterior fossa correlated to a higher frequence of tonsilar invagination, and with higher incidence of syringomyelia. Eight patients had brainstem auditory evoked potentials (BAEP) tests. 2 patients did not presented compression of neuro-axis; 2 showed compression and magnetic signal alteration, and 4 presented syringomyelia. One patient with compression and hyperintense signal in fluid sensitive sequences presented the greater delay in intervals I-III and I-V of auditory pathway. All patients with syringomyelia presented longer I-V interval, even after decompressive surgery. All patients with significant compromise to neural tissue showed assynchronic waves on binaural acquisition, with phase shift of wave V. MRI is an important tool to assess the morphological abnormalities of craniocervical junction. The discrepance between the duration of compressive injury and appearence of symptoms do not allow understand whether functional impairment is secondary to compressive state or to unknown neural tissue incipient malformations. BAEP analyses of these patients are not routinelly done, and these previous data demonstrated that the image and functional correlation can lead to unrevealing features of morphophysiology of the craniocervical juntion malformations.