Narcolepsy is a debilitating sleep disorder that affects up to 0.05% of individuals in Caucasian populations. It is highly associated with the HLA-DR2 group antigen or the HLA-DRB1*1501-DQB1*0602 haplotype, respectively. However, the HLA association by itself cannot sufficiently explain the increased risk to family members, as HLA-DR2 is quite common in the general population and most people harboring the respective genotype do not develop any symptoms of narcolepsy. Situated in the HLA class II region, the TNFA gene is translated into the pro-inflammatory cytokine TNF-alpha. TNFA promoter polymorphisms have been linked to several inflammatory and autoimmune diseases. We analyzed three SNP of the TNFA promoter and one adjacent microsatellite in 103 patients and 96 controls. The T-allele of the C-857T polymorphism was strongly associated with narcolepsy in the subgroup of DRB1*15/16 (HLA-DR2 type) negative patients, but not in DRB1*15/16 positive patients. These results point towards an etiological influence of TNFA alleles in narcolepsy and support previous findings suggesting genetic heterogeneity and differences in pathophysiological characteristics of HLA-DR2 positive and negative narcolepsy.