Crohn's disease (CD) appears in forms so diverse that it has been hypothesized CD might be a syndrome, with different pathogenic mechanisms leading to the various clinical phenotypes. This may plausibly explain the conflicting and inconclusive results with regard to HLA associations in unselected groups of patients. The power of these association studies may increase when disease heterogeneity is taken into account. As fistulising CD has been proposed as a separate subgroup of patients with CD, we studied the carrier frequencies (CF) of the DRB1 alleles in 35 unrelated Caucasian Dutch CD patients with proven peri-anal fistulas. A striking decrease in the frequency of the DRB1(*)03 allele was found in those patients with peri-anal fistulas when compared with a panel of 2400 healthy controls (HC) (3% vs 25%; P = 0.005; Odds Ratio [OR] = 0.09). The DRB1(*)03 allele is in strong linkage disequilibrium with a polymorphism at position -308 in the promoter region of the gene encoding TNFalpha (TNFA-308(*)2). We investigated whether this allele frequency was decreased as well. Surprisingly, the CF of TNFA-308(*)2 was 29%, not different from the CF of 98 HC (34%; P = 0. 7; OR = 0.8). This study is the first showing a significant negative association between DRB1(*)03 and a particular subgroup of CD patients. Thus, patient selection may largely determine the outcome of genetic association studies in CD, as we previously observed no association with this allele in an unselected population of CD patients. As DRB1(*)03 frequency, but not the closely linked TNFA-308(*)2, was decreased, this suggests recombination between the DRB1 and TNFA loci in this group of patients, and may help to define the biological basis of fistula formation.