Purpose Periodontitis causes low-grade systemic inflammation e.g., through circulatory periodontal endotoxins, and it has been associated with cardiovascular morbidity and wet age-related macular degeneration. Methods To assess the association between clinical severity of periodontitis and aqueous flare levels in the eyes. Patients with periodontitis (N = 15) who underwent periodontal treatment by a specialized dentist between the years 2020 and 2021 at the Chin and Mouth Disease Unit, Kymenlaakso Central Hospital, Kotka, Finland were enrolled. Aqueous flare levels, a surrogate marker for blood-aqueous and blood-retinal-barrier disruption, were measured using Laser Flare Meter (FM-600, Kowa Company, Ltd., Nagoya, Japan) before and right after the periodontal treatment and at 3 months. The number of teeth, periodontal probing depth (PPD), periodontal pathogens and antimicrobial treatment were recorded. Results At baseline, aqueous flare levels correlated with the number of clinically-relevant PPD (>5 mm) pockets (R = 0.789, P < 0.001) and inversely correlated with the number of teeth (R = −0.587, P = 0.035). At baseline, aqueous flare levels were 15.39 ± 13.24 photon units (pu)/ms among patients with periodontal pathogens, compared with 3.29 ± 1.67 pu/ms among those without any peridontal pathogens in PCR ( P = 0.018). At 3 months compared to baseline values, aqueous flare levels were reduced to <50% from baseline among 6 patients (40%), whereas the levels increased to >200% from baseline in 1 patient (7%) (repeated measures ANOVA, P < 0.026). Conclusions Poor periodontal status was associated with blood-ocular-barrier breakdown. These findings could expand our understanding of the potential mechanisms and therapeutic targets against retinal vascular diseases and systemic comorbidities in patients with periodontitis.