Increased activity in the sympathetic nervous system is part of the physiological stress response and is expressed in the heart rate variability (HRV). The objective of this study was to examine associations of HRV and intima media thickness (IMT). In 2002, satisfactory measurements of HRV of 78 voluntary participants were made, both during a stress test and during sleep. IMT in 2002 and the progression in IMT from 1998 to 2002 were analyzed in relation to measures of HRV. HRV was negatively associated with IMT and IMT progression both during test and sleep. In men with higher IMT measures than mean the low frequency-high frequency ratio was higher during sleep than during test, perhaps mirroring a lack of ability to recovery. HRV was negatively associated with IMT and IMT progression. HRV may be part of the pathophysiological pathway between psychological strain and atherosclerosis.