Background: Epidemiological studies have demonstrated associations between noise exposure and cardiovascular events. However, there have been few studies of possible underlying mechanisms. Objectives: We examined the association between individual day-time noise exposure and heart rate variability (HRV). Methods: In a prospective panel study in Augsburg, Germany (March 2007-December 2008), 110 individuals participated in 326 electrocardiogram recordings with a mean duration of six hours. Five-minute averages of heart rate (HR) and HRV parameters were determined. Individual noise exposure was measured as A-weighted equivalent continuous sound pressure levels (Leq). Effects were estimated using additive mixed models adjusted for long- and short-term time trends and physical activity. Due to non-linear exposure-response functions we performed piecewise linear analyses with a cut-off point at 65 dB(A). Results: Concurrent increases of 5dB(A) in Leq<65dB(A) were associated with increases in HR (%-change of mean value: 1.48%; 95% CI: 1.37, 1.60%) and the ratio of low frequency (LF) to high frequency (HF) power (4.89%; 95% CI: 3.48, 6.32%), and with decreases in LF (-3.77%; 95% CI: -5.49, -2.02%) and HF (-8.56%; 95% CI: -10.31, -6.78%) power. Standard deviation of normal-to-normal intervals (SDNN) was positively associated with concurrent noise <65dB(A) (5.74%; 95% CI: 5.13, 6.36) but negatively associated with noise lagged by five- to 15-minutes (-0.53% to -0.69%). Associations with cardiac function were less pronounced for noise ≥65dB(A), with some in opposite directions from associations with noise <65dB(A). Concurrent associations were modified by sex and age. Conclusions: Individual day-time noise exposure was associated with immediate changes in HRV, suggesting a possible mechanism linking noise to cardiovascular risk. Noise at lower levels may have health consequences beyond those resulting from “fight-or-flight” responses to high levels of noise.