Human leukocyte antigen (HLA) has been associated with Behcet's disease (BD), among which HLA-B51 is the most strongly associated genetic marker. The sandwich hybridization technique was applied in the design of the specific oligonucleotide probes to ensure the specific and accurate results. The probe-spotted chip was hybridized with the polymerase chain reaction (PCR) amplicons including nine suballeles (B5101-B5109) of exons 2 and 3 of HLA-B51 gene to determine the HLA-B51 genotypes. The results were subsequently confirmed by (PCR-SSP) and sequencing and were identical to those from polymerase chain reaction-sequencing specific primers (PCR-SSP) in 27 patients with BD and 30 healthy controls. This suggests that we successfully developed the oligochip for Behcet's-associated gene HLA-B51, which can effectively and accurately identify the HLA-B51 genotypes.