A common haplotype spanning 250 kb on chromosome 5q31 is strongly associated with Crohn disease (CD). Recently, two functional variants within theSLC22A4andSLC22A5genes at this locus (IBD5), L503F (c.1507C>T) and G-207C (c.-207G>C), have been proposed to contribute directly to susceptibility to CD. However, extensive linkage disequilibrium at theIBD5locus has complicated efforts to distinguish causal variants from association of the general risk haplotype. We genotyped theSLC22A4andSLC22A5variants and other polymorphisms across the risk haplotype in four populations of European origin, and applied regression-based haplotype analysis to over 1,200 fully genotyped case-control pairs, modeling case/control status on the presence of one or more SNPs to test for conditional association and to identify risk haplotypes. We found highly significant association of SNPs at theIBD5locus with Crohn disease in all populations tested. However, the frequencies of L503F and G-207C in individuals who did not carry the generalIBD5risk haplotype were not significantly different in cases and controls, with associated disease odds ratios (ORs) of 0.90 (95% CI, 0.57–1.40) and 0.90 (95% CI, 0.65–1.23), respectively. Haplotype analysis showed that addition of theSLC22A4andSLC22A5variants to a null model that included the background risk haplotype did not significantly improve the model fit. In addition to the common risk haplotype, several rare haplotypes had an increased frequency in cases compared to controls. This study suggests that the molecular basis for Crohn disease susceptibility at theIBD5locus remains to be defined, and highlights the challenge of the identification of causal variants in a complex disease in regions of extensive linkage disequilibrium. Hum Mutat 27(8), 778–785, 2006. Published 2006 Wiley-Liss, Inc.