We investigated the association of polymorphisms in the tumor necrosis factor (TNF) microsatellite as well as the promoter region of the TNFA gene and the TNFB gene with palmoplantar pustulosis (PPP). In order to clarify the heterogeneity of this disease, we performed a tonsillar provocation test on 78 patients and divided them into two groups according to the results; provocation positive (PP; n = 38) and provocation negative (PN; n = 40). We found that the phenotype frequency of the TNFB2 allele of the TNFB gene in the PN group was significantly higher than in controls (p = 0.0022, corrected p = 0.0044). There was also a significant increase in the frequency of allele B of the TNFA gene (TNFApB) in the PN group when compared with controls (p = 0.0049, corrected p = 0.025). Although there are no significant differences in the frequency of TNFa microsatellites, the frequency of the TNFd7 allele increased and that of the TNFd4 allele decreased in the PN group. An extended haplotype analysis revealed that the TNFd7-TNFApA-TNFB2 haplotype was more frequent in the PN group, implying that the PN group is associated with a low level of TNF-alpha production. These results indicate that detection of polymorphisms at the TNF locus may be a marker for determination of the heterogeneity of the disease, and that the allelic variation may influence the susceptibility.