Behçet's disease (BD) related amyloidosis is relatively rare. Serum amyloid A protein (SAA) protein gene polymorphism is one of the factors implicated in the pathogenesis of AA type amyloidosis. The aim of this study is to investigate SAA1 gene polymorphism in different patient groups: (1) BD related amyloidosis, (2) BD without amyloidosis, and (3) healthy controls. One hundred eleven patients from three main groups were included in the study: (1) BD related amyloidosis (n = 9), (2) BD without amyloidosis (n = 39), and (3) healthy controls (n = 63). Homozygous alpha/alpha is present in 78% of patients with BD and amyloidosis. The SAA1 alpha/alpha genotype is significantly more common among patients with BD and amyloidosis. This study demonstrated increased frequency of alpha/alpha genotype in BD related amyloidosis. To our knowledge, the relationship between alpha/alpha genotype and BD related amyloidosis was not studied previously. In conclusion, the SAA1 alpha/alpha genotype is a risk factor for amyloidosis in BD.