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Virtually all babies with meningomyelocele have an associated Arnold Chiari II malformation, meaning that a portion of the base of the brain (a part of the cerebellum) is displaced down into the spinal canal within the neck. This sometimes causes pressure on the underlying brain stem, which is also elongated and partially within the neck's spinal canal. The most common early symptom of this condition is respiratory stridor, often occurring within one or two weeks of birth. This usually disappears spontaneously within a few days, or at most three months. It may, occasionally, be associated with impaired function of the lower parts of the brain (difficulty in swallowing, intermittent apnea or cessation of breathing, etc.). In these cases, serious consideration must be given to surgical decompression, a procedure involving removal of the posterior arch of the upper spine overlying the malformation. Although this may lead to significant improvement, the results are not uniformly favorable, for it is often the most seriously afflicted infants who suffer from this complication.

Arnold Chiari malformation can also cause later neurological deterioration, most often in the adolescent years. It may be associated with intermittent apnea and loss of consciousness (sometimes confused with a seizure). In infants, these cases require a decompressive procedure that must be done on an emergent basis—children with these symptoms are in danger of sudden infant death due to apnea. In older children, other symptoms such as suboccipital pain and lower cranial nerve dysfunction may mandate decompression. The results of decompression in this age group are much more favorable than they are in infancy, and the symptoms are completely relieved in most cases.

In the past few years it has been recognized that a tethered spinal cord may cause progressive loss of function in the lower extremities any time after a child is 3 or 4 years old. Until recently it was assumed that those born with an L3 or L4 level often used a wheelchair as they got older simply as a matter of convenience. It is now understood that every child who has undergone closure of meningomyelocele has a tethered spinal cord, for the neural plate invariably becomes adherent to the surrounding dura. Most patients will probably not develop symptoms, but a significant number of ambulators will gradually deteriorate as a result of this phenomenon. However, if the cord is untethered as soon as symptoms develop, the likelihood of returning to the previous baseline is excellent.

It has been recognized for several years that rapidly evolving scoliosis may also be associated with a tethered spinal cord, even in the absence of lower extremity function. Therefore, any child with fast-moving scoliosis should have an untethering operation prior to a definitive orthopaedic procedure. If this is done before the scoliosis exceeds 30 degrees, there is an excellent possibility of reversal.

A few of these children will develop hydromyelia (water within the interior of the spinal cord), which is usually manifest clinically by rapidly evolving scoliosis (similar to tethered spinal cord). The hydromyelia may be drained by various techniques (all satisfactory), and the scoliosis will often be arrested.