Objective: The current study investigated individual growth in autonomy development across the adolescent transition, comparing the trajectories of children with and without spina bifida. Method: Individual growth curve modeling procedures were utilized to describe the developmental course of autonomy across four waves of data collection, from ages 9 to 15, and to test whether illness status [spina bifida vs. matched comparison group (N = 68 for both groups at Time 1)] would significantly predict individual variability in autonomy development. Potential moderators [child gender, SES, and Peabody Picture Vocabulary Test (PPVT) score] of the association between illness status and autonomy development were also examined. Results: Children with spina bifida demonstrated distinct developmental trajectories, though the nature of the group differences varied by type of autonomy development (emotional vs. behavioral), context (i.e. school vs. family), and reporter. Significant interactions with PPVT score and child gender were found. Conclusion: Overall, children with spina bifida show considerable developmental resiliency, but may lag behind their peers in specific areas of autonomy. Boys with spina bifida, and children with spina bifida who have lower than average levels of verbal intelligence, appear to be at greater risk for exhibiting delays in autonomy development.