Cognitive and motor problems are common in children with spina bifida (SB), particularly in those children with cerebral malformations (SBM). Little is known about how these conditions affect motor learning. This study examines motor sequence learning in children with SB, SBM, and healthy controls. Assessment consisted of neuropsychological tests, a simple drawing task, and a spatial motor sequence learning task. Implicit motor learning was unaffected in children with SB(M), and their sequence learning ability was also similar to that of controls. However, both groups (SB and SBM) showed impaired motor performance. The role of cerebellar malformation with SB(M) is discussed.