BACKGROUND: Epidemiological studies have shown associations between particulate matter (PM) and heart rate variability (HRV). OBJECTIVES: We investigated the effects of air pollution on the root mean square of successive differences (RMSSD) and the standard deviation of normal-to-normal intervals (SDNN) and effect modifications by single nucleotide polymorphisms (SNP). METHODS: Between March 2007 and December 2008 207 ECG recordings comprising 1153 1 h-intervals were measured in 61 individuals with type 2 diabetes or impaired glucose tolerance (IGT) from Augsburg, Germany. Associations between 1 h-averages of air pollutants (PM, sulphate, black carbon, and ultrafine particles) and ECG parameters were analyzed using additive mixed models. Genotypes of 139 SNPs supposed to be involved in cardiac rhythm were identified in the literature. Using regression trees for longitudinal data, SNPs associated with ECG parameters were determined and included as potential air pollution effect modifiers. RESULTS: We observed concurrent and lagged decreases in SDNN by about 2-5% in association with all air pollutants, especially in participants with at least one minor allele of rs332229. Increases in PM<2.5 μm (PM(2.5)) were associated with 4 h-lagged decreases of -6.6% [95%-confidence interval:-10.6;-2.6%] and -13.0% [-20.7;-5.1%] in SDNN in individuals with one or two minor alleles. We observed a -7.2% [-12.2;-1.8%] reduction in RMSSD associated with concurrent increases in PM(2.5.) Individuals with at least one minor allele of rs2096767 or at most one minor allele of rs2745967 exhibited stronger PM(2.5) effects. CONCLUSIONS: We identified a genetic predisposition in persons with diabetes or IGT making them potentially more susceptible to air pollutants with regard to changes in HRV.