Introduction: Primary sclerosing cholangitis (PSC) is a rare, chronic, and progressive cholestatic liver disease involving intra- and/or extrahepatic bile ducts. PSC in significant number of patients results in end stage liver diseases. Nearly 60 percent of PSC patients suffer from concomitant inflammatory bowel diseases (IBDs). Classically, IBDs are divided to two principle types, Crohn’s disease (CD) and ulcerative colitis (UC). However, with growing knowledge PSC associated IBD (PSC-IBD), it seems to be a rather distinct entity with specific genetics, clinical and microbiota characteristics. Areas covered: In this article we aim to review PSC-IBD unique characteristics from clinical, genetic and microbiota point of view. Expert opinion: PSC-IBD unique characteristics contribute to the notion that PSC-IBD could be a distinct entity. Acknowledgment of PSC-IBD as a novel entity necessitate designing new clinical guidelines in confirmation of diagnosis and developing novel therapeutic settings. Keywords: Primary sclerosing cholangitis, PSC associated IBD, inflammatory bowel diseases, PSC-IBD Article highlights: • PSC genetic susceptibility shows a distinct pattern compared to the IBD patients. • PSC-IBD colonic involvement in contrast to IBD is right sided and has more severe course. • Risk of malignancies in PSC-IBD patients is considerably higher compared to IBD patients. • Microbiota studies in PSC patients revealed a distinct microbiota pattern compared to the IBD patients.