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Abstract Background Chronic Recurrent Multifocal Osteomyelitis (CRMO) is a condition characterized by sterile bone inflammation, usually occurring in childhood. Although the etiology remains unclear, this condition has been associated with inflammatory bowel disease (IBD). Primary sclerosing cholangitis (PSC) and Autoimmune Hepatitis (AIH) are also uncommon pediatric conditions with a known association with IBD. Case presentation We present a unique case of a pediatric patient with an initial diagnosis of CRMO, with subsequent diagnosis of autoimmune hepatitis and PSC overlap, and eventually IBD. Conclusions Patients with CRMO may also develop PSC in addition to IBD, further highlighting the importance of IBD pathophysiology in both conditions. Clinical screening of associated gastrointestinal findings may be of value in patients with CRMO.