The purpose was to determine the utility of including neurovegetative symptoms in assessments of depression in youth with inflammatory bowel disease (IBD). Forty-one youth with IBD and concurrent depressive symptomatology were enrolled in an intervention trial and received either 9 modules of cognitive-behavioral therapy (PASCET-PI) or treatment as usual (TAU). Youth and their primary caregivers completed the Children's Depression Inventory (CDI) at pre- (T1) and posttreatment (T2). Disease severity measures and current steroid dosage were obtained at each timepoint. Change in the individual items of the CDI was compared across groups and examined in association with change in physical illness course. Paired sample t-tests revealed significant changes in CDI item scores from T1 to T2 for a majority of the depressive symptoms assessed in the PASCET-PI group, but not for the TAU group. These changes did not appear to be linked to changes in disease severity and/or steroid dosage across these same timepoints. The inclusion of somatic items in the assessment of depression in physically ill youth is important, as these symptoms seem to respond to psychotherapeutic intervention. The present results would suggest that improvements in depressive symptomatology are not solely related to improvements in the course of IBD and that these items do reflect an important part of the profile of depressive symptoms in youth with IBD. Future research is warranted to replicate present findings and explore the generalizability of these results to other pediatric illness populations.