We investigated the associations between within-visit blood pressure variability (BPV) and risk factors for cardiovascular disease (CVD). The study subjects included 17,795 people aged 40-74 years who underwent health check-ups in Aichi Prefecture, Japan, and completed two blood pressure measurements. Subjects were categorized into three groups according to the difference of systolic blood pressure (ΔSBP), namely, low-BPV (≤ 10 mmHg), moderate-BPV (11-20 mmHg), and high-BPV (> 20 mmHg). Subjects were also divided into three categories as those without prediabetes (glycosylated hemoglobin A1c [HbA1c] < 5.7%), prediabetes (HbA1c 5.7-6.4%) and diabetes (HbA1c ≥ 6.5% or under treatment for diabetes). The proportion of prediabetes and diabetes were significantly higher in subjects with high-BPV than in those with low-BPV after adjusting for age, sex, and mean SBP (odds ratio [95% confidence interval] was 1.16 [1.01-1.33] for prediabetes and 1.33 [1.06-1.66] for diabetes). Other CVD risk factors were not associated with high-BPV after the adjustment. In conclusion, increased within-visit BPV was significantly associated with the prevalence of prediabetes and diabetes, independent of mean SBP, in a large general population. Therefore, assessing BPV in a single visit may help to identify subjects at increased risk of impaired glycemic control.