The purpose of this study was to observe both the glycemic variability in abdominally obese men with normal glucose tolerance (NGT) and the relationship between glycemic variability and early atherosclerosis. This case-control study included 23 abdominally obese men (waist circumference (WC) ≥90 cm) and 23 nonabdominally obese men (WC <90 cm) with NGT who were between 20 and 50 years of age. All subjects were of the Han ethnicity. The cases and controls were age-matched. A continuous glucose monitoring system (CGMS) was used in this study. With the CGMS, the standard deviation of blood glucose (SDBG) and the mean amplitude of glucose excursion (MAGE) were calculated to estimate glycemic variability. The carotid intima-media thickness (CIMT) was used as a surrogate marker of early atherosclerosis. Mean blood glucose (MBG) (6.13 ± 0.94 vs. 5.55 ± 0.87 mmol/l), SDBG (0.89 ± 0.34 vs. 0.64 ± 0.24 mmol/l), MAGE (2.05 ± 0.83 vs. 1.57 ± 0.52 mmol/l), and CIMT (0.73 ± 0.12 vs. 0.67 ± 0.05 mm) were significantly higher in the abdominally obese men than in the nonabdominally obese men (P < 0.05). WC positively correlated with MBG (r = 0.302, P = 0.041), SDBG (r = 0.362, P = 0.013), MAGE (r = 0.302, P = 0.041), and CIMT (r = 0.487, P = 0.001). CIMT did not correlate with MBG (r = 0.206, P = 0.169), SDBG (r = 0.114, P = 0.450), and MAGE (r = 0.085, P = 0.574). After multivariate analysis, WC was still significantly associated with MBG (β = 0.025, P = 0.041), SDBG (β = 0.010, P = 0.013), MAGE (β = 0.019, P = 0.042), and CIMT (β = 0.008, P = 0.022). This study demonstrates that glycemic variability is increased in abdominally obese men with NGT. A relationship between glycemic variability and atherosclerosis was not observed in this study and requires further investigation.