Mucosal healing is increasingly recognized as an important treatment goal in Crohn's disease (CD). Data from colonic disease shows improved long-term outcomes in patients achieving complete mucosal healing. Little is currently known of this with respect to ileitis, which is increasingly diagnosed using small bowel capsule endoscopy. The study aimed to prospectively assess mucosal healing and deep remission rates in a cohort of symptomatic small bowel CD patients commencing biologic or immunomodulator therapy. Baseline demographics, quality of life questionnaires and Harvey-Bradshaw index were collected along with C-reactive protein and calprotectin. Capsule endoscopy Crohn's disease activity (CECDAI) index was used to assess ileitis severity. All parameters were reassessed at week 12. Results at baseline and week 12 were compared using two-tailed Wilcoxon analysis, P value less than 0.05 was considered significant. In total, 43 patients of 71 screened underwent 80 small bowel capsule endoscopies. On the basis of the CECDAI, 39 (90%) demonstrated active small bowel CD at baseline with 37 (86%) undergoing 12-week assessment. Overall there was a statistically significant symptomatic and biochemical improvement at week 12. Furthermore, 10 (27%) had demonstrated a normalization in CECDAI (<3.5), which was statistically significant (P<0.0005, 95% confidence interval 0.12-0.15). However, no patient had achieved full mucosal healing. In patients with active small bowel CD early symptomatic and biochemical response to treatment is not mirrored by mucosal healing. Repeat mucosal healing assessment in this cohort is warranted following a longer duration of treatment to identify potential mucosal healing and deep remission rates.