Background: Primary sclerosing cholangitis (PSC) is a significant risk factor for developing colorectal cancer (CRC) in patients with inflammatory bowel disease (IBD). While there are known genetic predispositions to both IBD and CRC individually, the hereditary predisposition to CRC in IBD patients remains underexplored. This study aims to assess the risk posed by germline variants (GVs) in cancer-predisposing genes in IBD patients, including those with IBD-PSC. Methods: We analyzed 3 cohorts of IBD patients (with and without PSC) who underwent whole exome sequencing (WES) at the Mayo Clinic. Patients were initially stratified based on their history of dysplasia, which included CRC, high-grade dysplasia (HGD), low-grade dysplasia (LGD), indefinite for dysplasia (IFD), and no dysplasia. Subjects with multiple types of dysplasia were categorized by the most severe type (CRC/HGD > LGD > IFD). Subsequently, germline variant identification was performed on 96 cancer-predisposing genes from the Mayo Clinic panel in cases (patients with CRC or HGD) and controls (patients without dysplasia). A 2:1 matching was conducted within each cohort. Controls were matched to cases based on age, where case age was defined as the age at dysplasia diagnosis (CRC or HGD), and control age was defined as the age at the last colonoscopy or colectomy (if performed for non-dysplasia indications). Controls with a greater age match than cases were prioritized for selection. Candidate variants were selected based on the following criteria: mean mapping quality ≥30, minimum read depth ≥10, supporting reads ≥5, variant allele frequency (VAF) ≥0.20, and minor allele frequency (MAF) < 0.0001. Results: For the IBD-no PSC cohort, 55 cases were matched with 110 controls, with a mean match age of 59±16 years in cases and 66±13 years in controls (p=0.05). In the IBD-PSC cohort, 72 cases were matched with 150 controls, with a mean match age of 52±15 years in cases and 56±15 years in controls (p=0.004). Analysis of cancer-related genes identified 33 pathogenic/likely pathogenic (P/LP) germline variants in 16 genes. The most commonly affected genes in PSC cases included CHECK2 (3 variants), MC1R (3 variants), BARD1 (2 variants), DIS3L2, LZTR1, NTHL1, MSH6, POT1, and RECQL4. In IBD-no PSC cases, common genes included MC1R, MET, MSH6, NF1, NTHL1, PALB2, and TMEM127 (1 variant each). IBD-PSC and IBD-no PSC cases had more autosomal dominant (AD) variants (12.8% and 12.7%, respectively) than controls (3.9% and 3.6%, respectively). Additionally, rare deleterious variants (RDVs) were observed in 31.9% of IBD-PSC and 27.3% of IBD-no PSC cases, compared to 30% and 21.8% of controls, respectively. Conclusions: Our study demonstrates that germline variants in cancer-predisposing genes are more prevalent in IBD cases, including those with PSC, compared to controls. These findings suggest a potential hereditary predisposition to colorectal cancer in IBD, warranting further investigation into personalized cancer surveillance strategies based on genetic risk.