NOD2/CARD15 and IL23R gene variants play an important role in the susceptibility to Crohn's disease (CD). Studies of genotype-phenotype relationship suggest that these variants are associated with the development of the disease and specific phenotype. Preliminary reports analyzing the association between these variants have never been made on Algerian CD's. In a case-control design, 204 Algerian with CD diagnosed for at least 5years and 201 controls were included were genotyped for single nucleotide polymorphisms (SNP) in the NOD2/CARD15 gene R702W (SNP8, rs2066844), G908R (SNP12, rs2066845) and IL23R R381Q (rs11209026) gene variants were determined using the TaqMan SNP genotyping assays. NOD2/CARD15 908R was carried by 3% of the patients and none in control subjects (χ²=8.6, P_c=0.003, OR=13.20). NOD2/CARD15 702W was associated to CD outcome (χ²=17.2, P_c=0.00003, OR=12.5) and early onset of disease (group A1, χ²=19.3, P_c=1.10⁻⁵, OR=14.05, P_M–H=2.10⁻⁶). IL23R 381Q variants was more frequent in CD's patients than controls (χ²=8, P_c=0.005, OR=3.48), it was associated to earlier onset (group A1, χ²=7.1, P_c=0.007, OR=1.04, P_M–H=0.002), extra-intestinal manifestations (EIM) outcome (χ²=10.6, P_c=0.001, OR=1.05, P_M–H=0.002) and ileocolonic location (χ²=6.8, P_c=0.009, OR=1.05, P_M–H=0.001). In this Algerian cohort, NOD2/CARD15 and IL23R variants were associated with CD's outcomes and linked to a particular clinical phenotype.