Behçet's disease (BD) is a multisystemic inflammatory disease believed to be triggered by microbial or environmental factors on a genetic platform. Clinically, it may have an impact on many body systems, including the mucocutaneous, ocular, articular, vascular, and neurological systems. In this study, we aimed to determine the HLA-B51 subtypes and their correlations with the clinical findings of BD. Fifty-one patients with BD and 44 gender- and age-matched healthy subjects were included in this study. The HLA-B51 subtypes of all participants were determined, and the correlations of the clinical manifestations of the disease with the HLA-B51 subtypes were analyzed. HLA-B51 positivity was found to be significantly higher in the patient group (P < 0.001, RR = 15.20), which had significantly more frequent HLA-B5101, HLA-B5102(01), HLA-B5109, and HLA-B5122 subtypes than the healthy subjects (all P < 0.05). Furthermore, considering the correlation between the genetic makeup and clinical findings, the HLA-B5109 subtype was found to be less frequent in patients with papulopustular skin lesions (P = 0.042). The frequency of HLA-B5103 was significantly higher in patients with central nervous system involvement (P = 0.015). There may be a relationship between HLA-B5102(01), HLA-B5109, and HLA-B5122 in addition to HLA-B51 and HLA-B5101(01) in Turkish patients with BD. The HLA-B5109 subtype can be protective against papulopustular lesion development; however, the HLA-B5103 subtype may pose a risk for neuro-Behçet development in BD.