ObjectiveLow heart rate variability (HRV), an indicator of autonomic nervous system dysfunction, has been associated with increased all-cause and cardiovascular mortality and incident stroke. However, the relationship between HRV and cerebral small vessel disease (CSVD) showed contradictory results. We aimed to examine the relationship of HRV and total burden of CSVD and each of the magnetic resonance imaging (MRI) markers of CSVD. MethodsWe recruited 435 patients who attended our hospital for physical examination between June 2020 and August 2021. All underwent 24-h Holter monitoring and MRI scan. The standard deviation of normal-to-normal intervals (SDNN) was selected as the method for HRV assessment. The presence of severe white matter hyperintensity, lacunes, and >10 enlarged basal ganglia perivascular spaces, and cerebral microbleeds were added for estimating the CSVD score (0-4). Multivariate logistic analyses was performed to assess whether HRV was independently associated with the burden of CSVD and each of the MRI markers of CSVD, with and without stratification by prevalent diabetes. ResultsThis study included 435 subjects with a mean age of 64.0 (57.0-70.0) years; 49.4% of the patients were male, and 122 (28.0%) had a history of diabetes. In multivariate analyses, lower SDNN was independently associated with total burden of CSVD and the presence of enlarged perivascular spaces in all subjects. According to diabetes stratification, lower SDNN was independently associated with total burden of CSVD and each MRI markers of CSVD separately only in the diabetic group. ConclusionsLower HRV was associated with total burden of CSVD and each MRI markers of CSVD separately among diabetic patients, but not among non-diabetic patients.