Anaemia is the most common extraintestinal manifestation of inflammatory bowel disease (IBD). Due to its multifactorial etiopathogenesis, the differential diagnosis and treatment of anaemia in IBD is a significant clinical problem. The main aim of our study was to assess the usefulness of laboratory parameters, including hepcidin, in differential diagnoses of anaemia in hospitalized IBD patients. This study also estimated the impact of anaemia on the length of hospitalization and its relationship with clinical data of analyzed patients. The study included 118 adult patients diagnosed with IBD-55 with ulcerative colitis (UC) and 63 with Crohn's disease (CD). Anaemia was significantly more frequent in patients with CD-42 (66.7%)-compared to 31 (56.4%) patients with UC (p = 0.033). The prevalence of anaemia increased significantly with the severity of IBD and the extent of inflammatory changes in the endoscopic examination. Hospitalization time was significantly longer in patients with anaemia, especially in the group with UC. Ferritin concentrations < 30 ng/mL were found only in 15 (20.55%) IBD patients (9 with UC and 6 with CD), and ferritin < 100 ng/mL was observed in 22 (30.14%) patients, equally frequent with UC and CD (p > 0.05). Significantly higher concentrations of transferrin were observed in patients with anaemia in the course of UC compared to CD (2.58 ± 0.90 g/L vs. 2.15 ± 0.82 g/L; p = 0.037). On the other hand, saturation of transferrin < 16% was equally common in UC and CD patients. In our study, hepcidin levels in anaemic UC patients were significantly lower compared to UC without anaemia (p = 0.042), with no similar differences in CD independently of anaemia presence (p = 0.565). To conclude, we observed a high incidence of anaemia in patients with IBD and its significant impact on the length of hospitalization in UC. Routinely determined single laboratory parameters are not sufficient for the differential diagnosis of anaemia, and a complex laboratory assessment, including of hepcidin levels, is necessary for the full picture of anaemia in the course of IBD.