Musculoskeletal manifestations in patients with inflammatory bowel disease (IBD) are common and associated with poorer outcomes. Hence, early detection is important to optimally tailor treatment. We aimed to determine the prevalence and distribution of inflammatory lesions in peripheral joints and entheses in newly diagnosed IBD patients. Patients with newly diagnosed IBD from a prospective population-based inception cohort were consecutively included. Data on musculoskeletal symptoms were collected by questionnaires and by structured rheumatological interview. Peripheral joints and entheses were assessed clinically and by ultrasound (US), using standardized definitions. Of 110 included patients (mean age: 42 years, 40% male, 70 with ulcerative colitis (UC), 40 with Crohn's disease (CD)), history of ≥1 musculoskeletal symptoms was reported by 49%. Clinical examination revealed peripheral musculoskeletal manifestations in 56 (52.3%) patients; 29 (27.1%) had ≥1 tender and/or swollen joints and 49 (45.8%) ≥1 tender entheses. Small peripheral joints were predominantly affected. US found inflammation in ≥1 joint or enthesis in 52 (49.5 %) patients; 29 (27.4 %) had US synovitis in ≥1 joint, while 36 (34%) US enthesitis. Fibromyalgia classification criteria were fulfilled in seven (7.9%) patients. There was no difference in clinical or US findings between patients with UC and CD, nor between patients with active and inactive IBD. Half of patients with newly diagnosed IBD had inflammation in their peripheral joints and/or entheses, documented by rheumatological clinical and ultrasound evaluations. This indicates a need for multidisciplinary collaboration to ensure an optimal therapeutic strategy for suppressing inflammation in all disease domains.