Background Inflammatory bowel diseases are associated with a variety of extra-intestinal manifestations. The most frequent of these is joint involvement, which affects 16–33 % of IBD patients. Our aim was to evaluate the ultrasound prevalence of sub-clinical joint and entheseal involvement in patients with IBD without musculoskeletal symptoms, and to correlate the US findings with clinical and laboratory variables. Methods We recorded the clinical and laboratory data of 76 patients with IBD, 20 patients with spondyloarthritis (SpA) and 45 healthy controls at three rheumatology centers. All of the IBD patients and healthy controls were clinically examined by a rheumatologist in order to confirm the absence of musculoskeletal symptoms, and all of the subjects underwent grey-scale (GS) and power Doppler (PD) US examinations of the second and third metacarpophalangeal joints, knees and lower limbs in order to detect joint or entheseal abnormalities. Results A total of 1410 entheseal sites and 1410 joints were evaluated by US. Of the 76 patients with IBD, 64 (84.1 %) had at least one GS entheseal abnormality, and 11 (13.9 %) had more than one PD-positive entheseal site; 32 (42.1 %) showed sub-clinical joint involvement. There was a significant difference between the IBD patients and healthy controls in terms of global entheseal, PD-positive entheseal, and joint involvement (p < 0.0001), but no difference between the IBD and SpA patients. Anti-neutrophil cytoplasmic antibodies predicted entheseal involvement in patients with IBD (OR 6.031; p = 0.015). Conclusions The prevalence of sub-clinical joint and entheseal involvement was higher in IBD patients than healthy controls, but there was no difference between the IBD and SpA patients.