Crohn's disease, an inflammatory bowel disease, is infrequently associated with epithelial and subepithelial corneal inflammation. However, deep stromal inflammation has not been described previously in association with Crohn's disease. We report on a 52-year-old male who suffered from anterior uveitis and deep stromal inflammation. Complete ocular and systemic workup revealed an active asymptomatic Crohn's colitis; no other possible cause for the ocular inflammation was found. We conclude that deep stromal inflammation, in addition to the previously reported corneal epithelial inflammation, may be associated with Crohn's disease.