Crohn’s disease (CD) and ulcerative colitis (UC), the 2 major forms of inflammatory bowel disease (IBD), develop from both genetic and environmental etiologies. Genetic etiologies were hypothesized by consistently identified familial clustering, increased risk in Ashkenazi Jews, and greater monozygotic versus dizygotic twin concordance rates.1 However, molecular genetic risk factors have now been established. The most well-replicated include 3 common functional mutations in the NOD2 gene (G908R, R702W, and Cins1007fs), the IBD5 risk haplotype on chromosome 5q31 (including functional polymorphisms on SLC22A4 and SLC22A5), and recently discovered risk polymorphisms in interleukin 23 receptor (IL23R) and the autophagy gene ATG16L1.2–10 It is noteworthy that these risk polymorphisms have been consistently observed in persons of European ancestry but have not been found to be risk factors in the Japanese, Korean, and Chinese populations.11–14 Consistent environmental risk factors include residence in Western industrialized countries, especially more northern latitudes, and increased CD but decreased UC risk from smoking.15 To understand the effect of the various established IBD risk factors on a population, to determine gene penetrance for genetic counseling purposes, and to determine interactions, it is best to assess these risk factors in a population-based study. Understanding gene penetrances and gene interaction for genetic counseling purposes is becoming increasingly more critical, with multiple companies now offering the public at large the opportunity to purchase CD gene testing so individuals can know their disease risk. We have previously reported an assessment of known risk factors of IBD family history, Jewish ethnicity, tobacco, geography, and the 3 common NOD2/CARD15 mutations in a study cohort drawn from the population-based University of Manitoba IBD Research Registry (UMIBDRR).15 In this population-based case-control study within a cohort, the increased odds ratio (OR) of developing CD from a single mutant NOD2 gene was 3.7 and 2 mutant genes was 40.0. For the first time, we reported that NOD2 mutation risks were independent of risks for CD family history (OR = 6.2), Jewish ethnicity (OR = 18.5), and smoking (OR = 3.0 for current and 1.7 for ex-smokers, respectively). Population-based NOD2 penetrance was 4.9% for 2 mutant chromosomes, 0.54% for a single mutant chromosome and 0.184% for persons wildtype for NOD2. NOD2 was also a risk for stricturing and internal fistulizing CD complications. We have now expanded our assessment of CD genetic risk factors in our population-based IBD registry to include the recent 3 additional CD genetic risk factors that have been consistently replicated: IBD5 risk haplotype including functional variants on SLC22A4 and SLC22A5 genes, IL23R gene variants including the protective missense polymorphism Arg381Gln, and the established associated coding variant on ATG16L1, Thr300Ala. We now report the population-based risk and penetrance of these more recently established molecular genetic risk factors in the context of NOD2 status, IBD family history, tobacco, and Jewish ethnicity. We have also explored their potential gene– gene interactions, assessed the relative strength of different risk alleles for IBD5 and IL23R, and have examined the effect of multiple risk alleles from different genes on CD risk in a defined nonreferral-based population.