Crohn's disease (CD) is a chronic intestinal inflammatory disorder. Its prevalence in Ashkenazi Jewish (AJ) population is higher than in non-Jewish Caucasians. Twenty-two single nucleotide polymorphisms (SNPs) at or near 10 CD-associated genes were evaluated and their association with CD status was assessed in the AJ cohort. Genetic risk scores based on the risk allele count alone and weighed by the effect size were generated and their predictive value was evaluated. Three NOD2, two IL23R, one IRGM and one PTGER4 SNPs were independently associated with CD risk. Carriage of ≥7 copies of these risk alleles or the weighted score of ≥7 correctly classified 92% and 83% of the controls, respectively; however, only 29% and 47% of the cases were identified as having the disease, respectively. This cutoff was associated with a >4-fold increase in CD risk. In the context of these findings, the role of genetic counseling in this disease is explored. Education, risk assessment and understanding of the limitations of genetic testing may benefit patients and their families. A CD genetic counseling model is proposed.