Delayed heart rate recovery (HRR) after exercise is an estimate of impaired parasympathetic activity, and an independent predictor of all-cause and cardiovascular mortality. Carotid atherosclerosis is associated with high risk of stroke. We tested the hypothesis that delayed HRR is associated with carotid atherosclerosis in a cross-sectional study of 13,051 middle-aged men (age 49.1짹8.9 yrs) who participated in a routine health examination program. Carotid atherosclerosis was defined as > 20% of stenosis or > 1.0mm of Intima-media thickness by B-mode ultrasonography. HRR was measured at 1 and 2 minutes (HRR1 and HRR2, respectively) after exercise (peak heart rate – 1 and 2 minute HRR). Carotid atherosclerosis was present in 1,181 men (11.1%). The mean (+ SD) of HRR1 was 24.8짹 8.9, and HRR2 was 52.4짹12.6. After adjustment for age, SBP, smoking, fasting glucose, and hs-C-Reactive Protein, men with carotid atherosclerosis had lower mean HRR1 (22.6짹 8.62) and HRR2 (46.5짹12.4) than subjects without atherosclerosis, (HRR1 = 24.4+ 8.68, HRR2 = 51.7 +12.3) (p<0.05 both).. In multivariable adjusted logistic regression models, the odds of developing low HRR2 (quartile 1 (<44) vs. quartile 4 (>=61) were 1.33 times (95% CI: 1.02 – 1.72) greater in men with atherosclerosis vs. those without atherosclerosis. HRR1 was not significant. These results suggest that delayed HRR, an index of decreased parasympathetic activity, is strongly associated with carotid atherosclerosis independent of established risk factors in middle-aged men.