Structural brain changes in gray and white matter have been found in adults with Crohn’s disease (CD). In adults, increased disease activity has also been associated with decreased cognitive performance. We have shown similar effects for pediatric CD, particularly for gray matter and associated cognitive and emotional functions. Underlying inflammation and steroid therapy have emerged as contributors, however, associations between brain structure and immune pathways have not been studied. We here aim to replicate earlier findings of brain involvement in pediatric CD, including study of white matter structures, and to elucidate the impact of immune response on the central nervous system.