Small ubiquitin-like modifier 4 (SUMO4) has been shown to have the potential to down-regulate NF-kappaB signal, leading to decreased transcription of pro-inflammatory cytokines. Recently, SUMO4 polymorphisms have been shown to be associated with several autoimmune diseases. In the present study, the association of SUMO4 polymorphisms with Behcet's disease (BD) was investigated. Our results showed a significantly increased frequency of the + 438 C allele and a significantly decreased frequency of the AGAT haplotype in BD patients (p=0.0002, corrected p=0.002; p=0.000015, corrected p=0.0002, respectively). Stratification analysis indicated that these significant associations only existed in the HLA-B51 negative subjects (p=0.004, corrected p=0.032; p=0.001, corrected p=0.016, respectively). The GGAC haplotype was negatively associated with HLA-B51 positive BD patients (p=0.0007, corrected p=0.011). In conclusion, SUMO4 +438 C allele is associated with susceptibility to BD in HLA-B51 negative patients, while the AGAT haplotype is protectively associated with BD in HLA-B51 negative patients. The GGAC haplotype is protectively associated with BD in HLA-B51 positive patients.