In saliva samples collected from 31 patients with Behçet disease (nine of whom also supplied a second sample following periodontal treatment), salivary microbial communities were notably less diverse than in samples from 15 healthy controls. The differences could not be explained by immunosuppressive medication use or HLA-B*5101–MICA (a Behçet disease risk allele) carrier status. Periodontal treatment improved oral health in patients with Behçet disease but had no short-term effect on salivary bacterial communities.