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Background: Crohn’s Disease (CD) and Ulcerative Colitis (UC) can be really considered systemic diseases since they are often associated with EIMs. In addition to the bowel, multiple other organs can be affected in IBD, including the bones and joints, skin, eyes and hepatobiliary system. The EIMs can occur prior to, in conjunction with, or subsequent to onset of IBD. The aim of this study was to investigate the prevalence of EIMs in IBD patients and the correlation between the presence of EIMs and the seat of CD. Methods: Three hundred and seven IBD patients, who referred to our centre from January 2004 to October 2012, were retrospectively studied. In each patient we recorded sex, age and the possible presence of EIMs. In CD patients we evaluated also the seat of disease, according to Montreal Classification. Three types of EIMs were considered: musculoskeletal manifestations (including axial and peripheral arthritis); dermatologic manifestations (including erythema nodosum, pyoderma gangrenosum and psoriasis); ocular manifestations (including uveitis and iridocyclitis) and sclerosing cholangitis. Each patient could have one or more manifestations. Results: We observed 161 patients with CD (mean age 43.4 years) and 146 with UC (mean age 47.1). One hundred and fifty-one were female (49%) and 156 were male (51%). We found 51 EIMs in 44 out of 307 patients with a prevalence of 16.6% (CD 22.3%, UC 10.2%). The prevalence of axial arthritis was 4% (CD 7.5%, UC 2%); peripheral arthritis was 3.5% (CD 4.3%, UC 2.7%); erythema nodosum was 2.6% (CD 3.7%, UC 1.3%); pyoderma gangrenosum was 1% (CD 0.3%, UC 1.3%); psoriasis was 2.2% (CD 2.4%, UC 2%); uveitis was 1.6% (CD 2.4%, UC 0.7%); iridocyclitis was 0.6% (CD 1.2%, UC 0%). No sclerosing cholangitis was found in our patients. Seven EIMs were found before the diagnosis of IBD, 34 after diagnosis and 10 were present at the time of diagnosis. The prevalence of EIMs in CD patients, according to the seat of disease was 21% for L1 patients, 17% for L2, 20% for L3 and 0% for L4. The correlation between the presence of EIMs and the seat of disease was not statistically significant. Conclusions: The prevalence of EIMs is in keeping with those reported in the literature. EIMs are more frequent in CD than UC and the musculoskeletal manifestations are the most common. EIMs are important in the management of patients with CD and UC. A multispecialty approach to the care of these patients can be helpful in optimizing management.