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Background Primary sclerosing cholangitis (PSC) is a rare liver cholestatic disease with unknown aetiology, severe clinical course and poor prognosis. PSC most often co-occurs with inflammatory bowel diseases (IBD), especially ulcerative colitis (UC). The aim of the study. We aimed to analyse the clinical course of patients diagnosed with PSC hospitalised in the Department of Gastroenterology, Medical University of Silesia in Katowice in 2009–2018. Methods The analysis included 30 patients, aged from 7 to 18 years (mean age 13.5 years), 21/30 boys (70%) and 9/30 girls (30%), diagnosed with PSC. The analysis included age of diagnosis, clinical symptoms, course of the disease, laboratory and imaging results and complications. Results The average diagnosis age was 13 years. 22/30(73.3%) patients suffered from UC and 4/30 (13.3%) were diagnosed with Crohn’s disease. 2/30 (6.66%) patients remained IBD-free. Among them 7/30(23.3%) had an overlap syndrome—primary sclerosing cholangitis and autoimmune hepatitis. At the time diagnosis 6/30 (20%) patients presented abdominal pain, which was the most common symptom, while 16/30 (57%) were asymptomatic but had abnormal laboratory test results. When PSC was detected before IBD, patients had complications more often compared with those diagnosed with IBD first or PSC and IBD at the same time. Moreover, complications were observed more often in patients with changes characteristic of PSC visible in their first USG than in patients without mentioned abnormalities in first USG. Conclusion Patients diagnosed with PSC before IBD diagnosis are more likely to have a more aggressive course of the disease. Monitoring liver markers in IBD patients is important since most PSC cases are asymptomatic and their elevation might be the first sign of the disease.