Deep and subcortical white matter hyperintensity (DSWMH) lesions are a small-vessel disease of the brain. The aim of this cross-sectional study was to investigate the relationship between DSWMH lesions and periodontal status in Japanese adults who participated in a health check. We enrolled 444 consecutive participants (mean age, 54.5 years) who received both brain and oral health evaluation services at the Asahi University Hospital. Magnetic resonance imaging was used to detect DSWMH lesions. Periodontal status was assessed using the community periodontal index. Of the study participants, 215 (48.4%) had DSWMH lesions. Multivariate logistic regression showed that the presence of DSWMH lesions was significantly related to age ≥ 65 years (vs. < 65 years, odds ratio [OR] = 2.984, 95% confidence interval [CI] = 1.696–5.232), systolic blood pressure ≥ 140 mmHg (vs. < 140 mmHg, OR = 2.579, 95% CI = 1.252–5.314), the presence of ≥ 28 teeth (vs. < 28 teeth, OR = 0.635, 95% CI = 0.420–0.961), and probing pocket depth (PPD) ≥ 6 mm (vs. PPD < 6 mm, OR = 1.948, 95% CI = 1.132–3.354) after adjustment for confounding factors. Having PPD ≥ 6 mm may be a risk factor for DSWMH lesions in Japanese adults.