IntroductionFistula formation in patients with Crohn’s disease is a common complication during the course of the disease. Perianal and enteroenteric are the most common forms of fistulas, whereas the involvement of the upper gastrointestinal tract with gastrocolic and duodenocolic fistulas represents an extremely unusual condition. Moreover, hyperthyroidism in association with Crohn’s disease has been rarely described.Case presentationWe present here a rare case of a 25-year-old male with simultaneous onset of hyperthyroidism and fistulizing Crohn’s disease. Crohn’s disease was complicated with intra-abdominal fistulas involving the upper gastrointestinal tract (duodenocolic, gastrocolic) and an intra-peritoneal abscess formation in the lesser sac. We describe the clinical presentation and therapeutic management of the patient including both medical treatment and surgical intervention. Despite intense medical treatment with total parenteral nutrition, antibiotics, aminosalicylates and corticosteroids the clinical course of the disease was suboptimal. Finally, the patient underwent laparotomy and right hemi-colectomy with ileo-transverse anastomosis performed, with simultaneous drainage of the abdominal abscess and primary closure of the upper gastrointestinal tract openings (gastric, duodenal and jejunal) at one stage operation. Although the surgical approach definitively cured the perforating complications of the disease (fistulas and abscess), the luminal disease in the colon remnant was still active and steroid-refractory. The subsequent successful treatment with infliximab, azathioprine and mesalazine resulted in the induction and maintenance of the disease remission. Thyrotoxicosis was successfully treated with methimazole and the hyperthyroidism has definitely subsided.ConclusionThe management of intra-abdominal fistulas in Crohn’s disease is a complex issue, requiring a multi-disciplinary approach and ‘tailoring’ of the treatment to the individual patient’s needs. Probably, a sensible approach involves early surgical intervention with prior optimization of the patient’s general condition when feasible. Common autoimmune mechanisms are probably involved in thyroid dysfunction associated with Crohn’s disease. Moreover, diagnosis and treatment of coexisting thyroid disorder in patients with Crohn’s disease has a favorable impact in disease prognosis.