Behçet's disease (BD) is a multi-systemic inflammatory disease. Previous reports indicated that MICA*009 confers susceptibility to BD. MICA*049 differs from MICA*009:01, a major MICA*009 subtype, only at codon 335 in exon 6. However, the potential association of MICA*049 with BD has not been addressed. In this study, we differentiated association among MICA*049, MICA*009 and HLA-B*51 with BD. A Han Chinese cohort consisting of 41 BD patients and 197 ethnically matched controls were examined with sequencing and T-ARMS-PCR for genotyping of MICA, and ARMS-PCR for HLA-B*51. The phenotype frequency of MICA*049 (41.5% versus 8.1%, OR = 8.01, P = 1.91 × 10-8) and HLA-B*51 (46.3% versus 15.7%, OR = 4.62, P = 1.21 × 10-5) were significantly higher in BD patients than those in controls, whereas MICA*009 showed no significant difference between the two groups (17.1% versus 13.2%, OR = 1.35, P = 0.51). After stratification for the effect of HLA-B*51, MICA*049 was still associated with BD in HLA-B*51 negative patients (OR = 40.61, P = 0.02). Our results indicate that MICA*049, not MICA*009, is a risk factor to BD, and that is independent from HLA-B*51 in the Han Chinese cohort.